Add files using upload-large-folder tool
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- RNA-seq/1-HEK293T-1_S1_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/1-HEK293T-1_S1_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/1-HEK293T-1_S1_salmon/cmd_info.json +17 -0
- RNA-seq/1-HEK293T-1_S1_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/1-HEK293T-1_S1_salmon/lib_format_counts.json +21 -0
- RNA-seq/1-HEK293T-1_S1_salmon/logs/salmon_quant.log +61 -0
- RNA-seq/10-HS707A_S10_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/10-HS707A_S10_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/10-HS707A_S10_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/10-HS707A_S10_salmon/logs/salmon_quant.log +53 -0
- RNA-seq/11-MCF7_S11_L001_R1_001.fastq.gz +3 -0
- RNA-seq/11-MCF7_S11_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/11-MCF7_S11_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/11-MCF7_S11_salmon/cmd_info.json +17 -0
- RNA-seq/11-MCF7_S11_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/11-MCF7_S11_salmon/lib_format_counts.json +21 -0
- RNA-seq/11-MCF7_S11_salmon/logs/salmon_quant.log +56 -0
- RNA-seq/12-ZR-75-1_S12_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/12-ZR-75-1_S12_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/12-ZR-75-1_S12_salmon/cmd_info.json +17 -0
- RNA-seq/12-ZR-75-1_S12_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/12-ZR-75-1_S12_salmon/lib_format_counts.json +21 -0
- RNA-seq/12-ZR-75-1_S12_salmon/logs/salmon_quant.log +58 -0
- RNA-seq/13-A549_S13_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/13-A549_S13_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/13-A549_S13_salmon/cmd_info.json +17 -0
- RNA-seq/13-A549_S13_salmon/lib_format_counts.json +21 -0
- RNA-seq/14-BxPC3_S14_L001_R1_001.fastq.gz +3 -0
- RNA-seq/14-BxPC3_S14_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/14-BxPC3_S14_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/14-BxPC3_S14_salmon/cmd_info.json +17 -0
- RNA-seq/14-BxPC3_S14_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/14-BxPC3_S14_salmon/lib_format_counts.json +21 -0
- RNA-seq/14-BxPC3_S14_salmon/logs/salmon_quant.log +52 -0
- RNA-seq/15-Colo320_S15_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/15-Colo320_S15_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/15-Colo320_S15_salmon/cmd_info.json +17 -0
- RNA-seq/15-Colo320_S15_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/15-Colo320_S15_salmon/lib_format_counts.json +21 -0
- RNA-seq/15-Colo320_S15_salmon/logs/salmon_quant.log +56 -0
- RNA-seq/16-HCC44_S16_L001_R1_001.fastq.gz +3 -0
- RNA-seq/16-HCC44_S16_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/16-HCC44_S16_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/16-HCC44_S16_salmon/cmd_info.json +17 -0
- RNA-seq/16-HCC44_S16_salmon/libParams/flenDist.txt +2 -0
- RNA-seq/16-HCC44_S16_salmon/lib_format_counts.json +21 -0
- RNA-seq/16-HCC44_S16_salmon/logs/salmon_quant.log +54 -0
- RNA-seq/17-HEK293T-3_S17_salmon/aux_info/ambig_info.tsv +0 -0
- RNA-seq/17-HEK293T-3_S17_salmon/aux_info/meta_info.json +44 -0
- RNA-seq/17-HEK293T-3_S17_salmon/cmd_info.json +17 -0
RNA-seq/1-HEK293T-1_S1_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/1-HEK293T-1_S1_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 758085,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 19791519,
|
| 35 |
+
"num_mapped": 10316668,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 71901,
|
| 38 |
+
"num_fragments_filtered_vm": 453017,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 4172252,
|
| 40 |
+
"percent_mapped": 52.1267114464534,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 13:02:51 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 13:04:56 2020"
|
| 44 |
+
}
|
RNA-seq/1-HEK293T-1_S1_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"1-HEK293T-1_S1_L001_R1_001.fastq.gz",
|
| 8 |
+
"1-HEK293T-1_S1_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"1-HEK293T-1_S1_L001_R2_001.fastq.gz",
|
| 12 |
+
"1-HEK293T-1_S1_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "1-HEK293T-1_S1_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/1-HEK293T-1_S1_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
2.44601e-44 3.64591e-44 5.42573e-44 8.0615e-44 1.19586e-43 1.77112e-43 2.61891e-43 3.86633e-43 5.69879e-43 8.38633e-43 1.23216e-42 1.80745e-42 2.6471e-42 3.87062e-42 5.65061e-42 8.23599e-42 1.19851e-41 1.74129e-41 2.52585e-41 3.65804e-41 5.28926e-41 7.63566e-41 1.10053e-40 1.58367e-40 2.27527e-40 3.26367e-40 4.67394e-40 6.68293e-40 9.54014e-40 1.35972e-39 1.93485e-39 2.74885e-39 3.89906e-39 5.52172e-39 7.80717e-39 1.10209e-38 1.55327e-38 2.18566e-38 4.72537e-20 1.82594e-12 3.53592e-07 1.41435e-06 2.12188e-06 1.5169e-06 1.1472e-06 2.24963e-06 3.15106e-06 2.67021e-06 2.73351e-06 5.46482e-06 1.0504e-05 2.34971e-05 5.95916e-05 0.000114778 0.000164009 0.000204183 0.000239012 0.000246936 0.000221064 0.000187389 0.000169044 0.000171449 0.000187435 0.00020572 0.000215892 0.000212893 0.000209263 0.000221937 0.000248331 0.000269716 0.000272658 0.00026573 0.000267215 0.000290836 0.000335847 0.000376363 0.000410104 0.000479032 0.000613262 0.000782563 0.000877581 0.000835585 0.000724906 0.000622717 0.000570869 0.000620863 0.000783298 0.000915619 0.000877849 0.000774304 0.000743458 0.000756604 0.000759974 0.000758846 0.000778779 0.000825552 0.000882133 0.000938626 0.000999826 0.00105504 0.00107206 0.00106809 0.00110514 0.00118071 0.0012487 0.00130574 0.00135876 0.0013991 0.00143265 0.00147889 0.00155441 0.00165279 0.00174673 0.00181117 0.00185337 0.00191401 0.00200455 0.0021065 0.00220029 0.00226157 0.00230407 0.00237573 0.00249119 0.00261996 0.00273259 0.00283361 0.00294196 0.00307092 0.00321639 0.00334655 0.00343943 0.00352327 0.0036493 0.00380207 0.00388919 0.00389991 0.00393827 0.00403104 0.00410986 0.00416087 0.00419561 0.00421431 0.00426003 0.00432823 0.00438552 0.00449586 0.00466807 0.00478831 0.00483389 0.00485361 0.00485014 0.00491937 0.00512663 0.00525496 0.005163 0.00503655 0.00501899 0.00507835 0.0051748 0.0052728 0.00536235 0.005484 0.00561079 0.00569185 0.00579168 0.00593547 0.0060588 0.00610503 0.00603585 0.00595909 0.00599259 0.00605452 0.00604787 0.00606268 0.00625778 0.00652192 0.00675681 0.00717003 0.00763348 0.00769726 0.00732327 0.00682101 0.00638463 0.00603752 0.00581102 0.00571448 0.00565843 0.00560747 0.00564297 0.00588926 0.00635664 0.00667974 0.00651397 0.0061399 0.00592786 0.00578355 0.00560881 0.00552419 0.00554235 0.0055291 0.00542354 0.00533082 0.00532685 0.0053333 0.00534966 0.00548759 0.00570845 0.00577572 0.00558168 0.00532462 0.00518082 0.00512088 0.00506552 0.00499132 0.00493622 0.00491677 0.00491348 0.00492975 0.00493644 0.00486692 0.00474198 0.00464567 0.00460456 0.0046016 0.00460033 0.00457086 0.00452984 0.00446913 0.00437993 0.00432805 0.00432953 0.00429848 0.00419536 0.00408449 0.00402731 0.0040146 0.00404233 0.00412766 0.00418956 0.00411571 0.0039629 0.00387802 0.00387217 0.00385553 0.00381099 0.00376817 0.00373255 0.00372026 0.0037165 0.00367194 0.00359859 0.00352888 0.00346129 0.00340219 0.00335441 0.00330703 0.00326501 0.00324595 0.00325513 0.00327815 0.0032768 0.0032253 0.00315421 0.00308043 0.00299843 0.00294059 0.00291637 0.00291322 0.00291728 0.00287784 0.00280582 0.00276112 0.00273316 0.00271572 0.0027195 0.00270037 0.0026495 0.00261998 0.00260196 0.00254136 0.00245989 0.00242045 0.00242621 0.00243335 0.00244146 0.00247278 0.00247285 0.00240137 0.00233508 0.00231943 0.00229847 0.00225212 0.00220276 0.00215496 0.00213327 0.00215037 0.00216268 0.00213612 0.00209125 0.00205256 0.00201393 0.00198551 0.00198152 0.0019799 0.00196461 0.00192146 0.0018419 0.00176949 0.00174404 0.00176603 0.00179969 0.00177238 0.00168854 0.00163352 0.00162772 0.00163337 0.00162241 0.00159231 0.00157523 0.001579 0.00155492 0.00149066 0.0014343 0.00140871 0.0014017 0.00139424 0.00138138 0.00138315 0.00139643 0.00138995 0.00135778 0.00132433 0.0013136 0.0013347 0.00136469 0.00136972 0.00135695 0.00133766 0.00129733 0.00125051 0.00123312 0.00123204 0.00120838 0.0011728 0.00115446 0.00114827 0.00113381 0.00109923 0.00106293 0.0010488 0.00104542 0.00104688 0.00105985 0.00106113 0.00103579 0.00101047 0.00100132 0.000998182 0.000990211 0.000965259 0.000932788 0.000903573 0.000862816 0.000836082 0.000853685 0.000876835 0.000879137 0.000885475 0.000893328 0.000872156 0.000830357 0.000802258 0.000799806 0.000806405 0.000803306 0.000795333 0.000796188 0.000806139 0.000808418 0.000789745 0.000771466 0.000773219 0.000773447 0.000762495 0.00076099 0.0007668 0.000754783 0.000719265 0.000686027 0.000675987 0.000677054 0.000675632 0.000675922 0.000676221 0.00066669 0.000652126 0.000643971 0.000633678 0.00061675 0.000610064 0.000607987 0.000594986 0.000586819 0.000583449 0.000565949 0.000555266 0.000567514 0.000567424 0.000546383 0.000544837 0.000562164 0.000567222 0.000562415 0.000553577 0.000531445 0.000498326 0.000473203 0.000468611 0.000476688 0.000487266 0.000497559 0.00050817 0.000512051 0.000497338 0.000475909 0.0004646 0.000452944 0.000436776 0.000432783 0.000441917 0.00044678 0.000432682 0.000406855 0.000398192 0.000406245 0.00040633 0.000408924 0.000425049 0.000430551 0.000417422 0.000406468 0.000406815 0.000401368 0.000372694 0.000334147 0.000311656 0.000311228 0.000326945 0.000345494 0.000348753 0.000335659 0.000315895 0.000300029 0.000300359 0.000312485 0.000321812 0.000322639 0.000313617 0.000297542 0.000285701 0.000287291 0.000289906 0.000280374 0.000272231 0.000270009 0.000262708 0.000256237 0.000255821 0.000254342 0.000250415 0.00024859 0.000251982 0.000258836 0.000261406 0.000252679 0.000238535 0.000235329 0.000242829 0.000242093 0.000232981 0.000230011 0.000228637 0.000225408 0.000236196 0.000260389 0.000270413 0.000256407 0.000243741 0.00024815 0.000250642 0.000236883 0.000223931 0.00022332 0.000217492 0.000202641 0.000202417 0.000218356 0.000221676 0.000202682 0.000185102 0.000179286 0.000171547 0.000162601 0.000162362 0.000166874 0.000165885 0.000159335 0.000157975 0.000162572 0.000162345 0.000157599 0.000160759 0.000177509 0.000195424 0.000196661 0.000183111 0.000170394 0.000163092 0.000154974 0.000143356 0.000136516 0.000141509 0.00014806 0.000146469 0.000143929 0.000145197 0.000146618 0.000146008 0.000141603 0.00013706 0.000135987 0.000134483 0.000132138 0.000128954 0.000123981 0.000123027 0.000127778 0.000131886 0.000134147 0.000138008 0.000139207 0.000132403 0.000125964 0.000126656 0.000126946 0.000121631 0.000112822 0.000103703 9.90809e-05 0.00010218 0.000107007 0.000105864 0.000102282 9.88863e-05 9.12271e-05 8.41718e-05 8.67417e-05 9.33532e-05 9.647e-05 0.000100357 0.000102289 9.65021e-05 9.34724e-05 9.45842e-05 8.82939e-05 8.06509e-05 8.10496e-05 8.5684e-05 8.80581e-05 8.27195e-05 7.34651e-05 7.28436e-05 7.97206e-05 8.04875e-05 7.54878e-05 7.38782e-05 7.62642e-05 8.15071e-05 8.41645e-05 7.79369e-05 7.23319e-05 7.53584e-05 7.98287e-05 7.90942e-05 7.45337e-05 7.13368e-05 7.11273e-05 7.2318e-05 7.53422e-05 7.87333e-05 7.94246e-05 7.9086e-05 7.9971e-05 8.13494e-05 8.06986e-05 7.6345e-05 7.23245e-05 7.06951e-05 6.89258e-05 6.63904e-05 6.36472e-05 6.42467e-05 6.77888e-05 6.62768e-05 5.80044e-05 5.1151e-05 5.22241e-05 5.76787e-05 6.1125e-05 5.87798e-05 5.06876e-05 4.50276e-05 4.61131e-05 4.85238e-05 4.95396e-05 5.16681e-05 5.67139e-05 6.15496e-05 6.20174e-05 5.94381e-05 5.6666e-05 5.41083e-05 5.0577e-05 4.64627e-05 4.54977e-05 4.73926e-05 4.82368e-05 4.96425e-05 5.2935e-05 5.37345e-05 5.17572e-05 5.08766e-05 4.94387e-05 4.4445e-05 4.08689e-05 4.58839e-05 5.56455e-05 6.02237e-05 5.73154e-05 5.05782e-05 4.54129e-05 4.52143e-05 4.81816e-05 5.09727e-05 4.97194e-05 4.53356e-05 4.38323e-05 4.44841e-05 4.28822e-05 3.94082e-05 3.68344e-05 3.69107e-05 3.82904e-05 3.93575e-05 3.96612e-05 3.6986e-05 3.17759e-05 2.91545e-05 3.07643e-05 3.53187e-05 4.23905e-05 4.70093e-05 4.325e-05 3.46219e-05 2.95094e-05 2.88029e-05 3.03758e-05 3.44289e-05 3.59051e-05 3.34115e-05 3.4275e-05 3.73762e-05 3.65374e-05 3.28425e-05 2.73885e-05 2.06614e-05 1.78855e-05 2.17829e-05 2.76585e-05 3.00964e-05 2.90566e-05 2.77309e-05 2.80118e-05 3.02484e-05 3.2588e-05 3.20425e-05 2.92425e-05 2.4753e-05 1.89691e-05 1.68832e-05 1.98618e-05 2.45043e-05 2.91436e-05 3.14039e-05 2.99074e-05 2.62346e-05 2.19103e-05 1.92343e-05 2.10923e-05 2.6615e-05 2.91667e-05 2.47151e-05 1.90103e-05 1.77361e-05 1.91136e-05 2.05022e-05 2.15458e-05 2.20064e-05 2.26359e-05 2.53882e-05 2.94026e-05 3.08957e-05 2.82779e-05 2.3375e-05 2.03924e-05 2.09668e-05 2.05821e-05 1.72938e-05 1.40062e-05 1.16386e-05 1.09705e-05 1.3095e-05 1.59017e-05 1.6716e-05 1.58265e-05 1.62071e-05 1.85492e-05 1.95624e-05 1.76723e-05 1.48958e-05 1.43705e-05 1.59376e-05 1.63495e-05 1.60216e-05 1.61065e-05 1.55889e-05 1.60006e-05 1.77711e-05 1.87272e-05 1.93688e-05 2.02422e-05 1.99014e-05 1.87636e-05 1.8065e-05 1.77898e-05 1.75624e-05 1.65722e-05 1.56561e-05 1.70691e-05 1.97549e-05 2.04513e-05 1.8468e-05 1.59163e-05 1.46274e-05 1.51645e-05 1.78812e-05 2.09428e-05 2.12814e-05 1.95661e-05 1.78235e-05 1.64848e-05 1.66589e-05 1.8314e-05 1.83121e-05 1.46179e-05 1.05195e-05 1.04669e-05 1.20624e-05 1.10664e-05 1.00855e-05 1.17794e-05 1.45779e-05 1.75325e-05 1.85692e-05 1.5549e-05 1.08589e-05 7.9193e-06 8.03915e-06 1.07739e-05 1.39438e-05 1.50851e-05 1.364e-05 1.21302e-05 1.31663e-05 1.5338e-05 1.52571e-05 1.29638e-05 1.15235e-05 1.08603e-05 9.78208e-06 1.006e-05 1.06914e-05 1.04697e-05 1.23075e-05 1.4195e-05 1.29269e-05 1.25526e-05 1.36316e-05 1.2167e-05 1.02487e-05 1.07185e-05 1.12094e-05 1.13314e-05 1.31659e-05 1.39859e-05 1.10262e-05 7.96964e-06 7.60096e-06 8.46751e-06 9.96704e-06 1.10584e-05 1.07356e-05 1.24289e-05 1.69456e-05 1.78244e-05 1.35866e-05 1.06081e-05 1.12464e-05 1.24891e-05 1.30579e-05 1.41138e-05 1.3776e-05 9.74608e-06 5.92272e-06 6.14271e-06 8.55478e-06 9.62454e-06 9.07196e-06 8.80193e-06 8.26927e-06 6.99489e-06 6.45708e-06 6.94805e-06 7.9297e-06 8.54355e-06 7.21362e-06 4.63607e-06 3.48881e-06 4.04972e-06 5.71301e-06 8.14522e-06 9.13002e-06 7.96302e-06 6.58322e-06 6.29575e-06 7.1903e-06 7.9557e-06 7.68805e-06 6.92277e-06 5.99704e-06 5.88714e-06 7.86247e-06 1.11741e-05 1.30503e-05 1.18663e-05 9.78774e-06 9.20818e-06 8.9981e-06 8.48769e-06 8.63535e-06 8.27891e-06 6.98273e-06 6.45538e-06 6.58799e-06 6.48871e-06 6.57161e-06 6.54995e-06 5.46354e-06 4.0026e-06 3.79461e-06 4.76183e-06 5.13171e-06 4.32849e-06 3.81318e-06 4.07301e-06 4.06265e-06 4.99264e-06 8.4022e-06 1.07539e-05 9.00283e-06 6.38502e-06 6.26438e-06 8.53051e-06 1.10053e-05 1.07966e-05 8.75718e-06 8.13427e-06 8.25146e-06 7.19971e-06 6.16314e-06 6.28152e-06 6.94501e-06 7.07278e-06 6.22062e-06 5.32261e-06 4.75304e-06 4.02334e-06 3.56747e-06 4.16586e-06 5.61098e-06 6.40747e-06 5.61985e-06 4.42055e-06 4.11771e-06 4.5285e-06 5.05583e-06 5.14156e-06 4.95764e-06 5.60352e-06 6.5791e-06 6.27314e-06 4.83369e-06 4.01882e-06 4.50581e-06 4.65348e-06 3.89576e-06 4.37611e-06 6.18785e-06 6.1291e-06 4.02411e-06 3.01569e-06 3.75845e-06 5.15363e-06 6.1272e-06 5.61042e-06 4.42768e-06 3.93692e-06 4.05843e-06 4.21737e-06 4.67067e-06 6.36469e-06 8.33765e-06 8.1546e-06 5.69477e-06 3.59168e-06 4.22067e-06 7.2339e-06 1.02192e-05 1.03837e-05 7.23819e-06 3.81805e-06 2.74772e-06 3.6973e-06 4.39363e-06 3.8027e-06 3.63633e-06 4.36023e-06 4.59908e-06 4.26545e-06 3.79336e-06 3.41287e-06 3.52956e-06 3.70362e-06 3.30417e-06 2.90844e-06 3.31156e-06 3.57951e-06 2.66182e-06 1.94055e-06 2.69591e-06 4.34281e-06 6.07443e-06 7.33969e-06 7.21438e-06 5.38821e-06 4.08038e-06 4.72533e-06 4.89985e-06 3.36705e-06 2.37079e-06 2.78865e-06 3.05596e-06 2.53634e-06 2.18144e-06 2.6471e-06 3.3186e-06 3.53414e-06 3.82705e-06 4.55128e-06 5.09616e-06 4.79171e-06 3.47441e-06 2.23298e-06 2.14449e-06 2.85423e-06 3.80647e-06 4.88123e-06 5.48526e-06 4.75517e-06 3.56653e-06 3.38501e-06 3.5188e-06 3.10564e-06 2.63732e-06 2.23662e-06 1.94665e-06 2.27244e-06 2.83721e-06 0.000109484 0.000429081 0.000641897
|
| 2 |
+
|
RNA-seq/1-HEK293T-1_S1_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 1-HEK293T-1_S1_L001_R1_001.fastq.gz, 1-HEK293T-1_S1_L001_R2_001.fastq.gz], [ 1-HEK293T-1_S1_L002_R1_001.fastq.gz, 1-HEK293T-1_S1_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 10316668,
|
| 6 |
+
"num_assigned_fragments": 10316668,
|
| 7 |
+
"num_frags_with_consistent_mappings": 8568749,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 1747919,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 8568749,
|
| 15 |
+
"SF": 685006,
|
| 16 |
+
"SR": 1062913,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/1-HEK293T-1_S1_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,61 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 13:02:51.086] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 13:02:51.165] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 13:02:51.167] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 13:02:58.898] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 13:02:58.898] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 13:03:48.024] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
|
| 12 |
+
[2020-11-04 13:03:48.039] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
|
| 13 |
+
[2020-11-04 13:03:48.059] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
|
| 14 |
+
[2020-11-04 13:03:48.088] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
|
| 15 |
+
[2020-11-04 13:03:48.098] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
|
| 16 |
+
[2020-11-04 13:03:48.101] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
|
| 17 |
+
[2020-11-04 13:03:48.103] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
|
| 18 |
+
[2020-11-04 13:03:48.111] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
|
| 19 |
+
[2020-11-04 13:03:48.123] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
|
| 20 |
+
[2020-11-04 13:03:48.134] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
|
| 21 |
+
[2020-11-04 13:03:48.142] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
|
| 22 |
+
[2020-11-04 13:03:48.157] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
|
| 23 |
+
[2020-11-04 13:03:48.785] [fileLog] [info]
|
| 24 |
+
At end of round 0
|
| 25 |
+
==================
|
| 26 |
+
Observed 19791519 total fragments (19791519 in most recent round)
|
| 27 |
+
|
| 28 |
+
[2020-11-04 13:03:48.785] [jointLog] [info] Computed 758,085 rich equivalence classes for further processing
|
| 29 |
+
[2020-11-04 13:03:48.785] [jointLog] [info] Counted 10,316,668 total reads in the equivalence classes
|
| 30 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] Number of mappings discarded because of alignment score : 4,172,252
|
| 31 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 453,017
|
| 32 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 33 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 71,901
|
| 34 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] Mapping rate = 52.1267%
|
| 35 |
+
|
| 36 |
+
[2020-11-04 13:03:48.803] [jointLog] [info] finished quantifyLibrary()
|
| 37 |
+
[2020-11-04 13:03:48.805] [jointLog] [info] Starting optimizer
|
| 38 |
+
[2020-11-04 13:04:01.596] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 13:04:01.630] [jointLog] [info] iteration = 0 | max rel diff. = 3567.49
|
| 40 |
+
[2020-11-04 13:04:04.655] [jointLog] [info] iteration = 100 | max rel diff. = 12.72
|
| 41 |
+
[2020-11-04 13:04:07.641] [jointLog] [info] iteration = 200 | max rel diff. = 17.7229
|
| 42 |
+
[2020-11-04 13:04:10.717] [jointLog] [info] iteration = 300 | max rel diff. = 1.88919
|
| 43 |
+
[2020-11-04 13:04:13.681] [jointLog] [info] iteration = 400 | max rel diff. = 0.2253
|
| 44 |
+
[2020-11-04 13:04:16.643] [jointLog] [info] iteration = 500 | max rel diff. = 1.66062
|
| 45 |
+
[2020-11-04 13:04:19.617] [jointLog] [info] iteration = 600 | max rel diff. = 9.50988
|
| 46 |
+
[2020-11-04 13:04:22.565] [jointLog] [info] iteration = 700 | max rel diff. = 5.16145
|
| 47 |
+
[2020-11-04 13:04:25.545] [jointLog] [info] iteration = 800 | max rel diff. = 0.0809726
|
| 48 |
+
[2020-11-04 13:04:28.532] [jointLog] [info] iteration = 900 | max rel diff. = 0.0450134
|
| 49 |
+
[2020-11-04 13:04:31.485] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0606601
|
| 50 |
+
[2020-11-04 13:04:34.368] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0375022
|
| 51 |
+
[2020-11-04 13:04:37.336] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.776045
|
| 52 |
+
[2020-11-04 13:04:40.303] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.266075
|
| 53 |
+
[2020-11-04 13:04:43.317] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.346001
|
| 54 |
+
[2020-11-04 13:04:46.394] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.20014
|
| 55 |
+
[2020-11-04 13:04:49.456] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.149391
|
| 56 |
+
[2020-11-04 13:04:52.512] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.0392946
|
| 57 |
+
[2020-11-04 13:04:55.579] [jointLog] [info] iteration = 1,800 | max rel diff. = 0.0749323
|
| 58 |
+
[2020-11-04 13:04:56.006] [jointLog] [info] iteration = 1,815 | max rel diff. = 0.00642309
|
| 59 |
+
[2020-11-04 13:04:56.028] [jointLog] [info] Finished optimizer
|
| 60 |
+
[2020-11-04 13:04:56.028] [jointLog] [info] writing output
|
| 61 |
+
|
RNA-seq/10-HS707A_S10_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/10-HS707A_S10_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 431642,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 9522549,
|
| 35 |
+
"num_mapped": 6514484,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 42813,
|
| 38 |
+
"num_fragments_filtered_vm": 150183,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 911361,
|
| 40 |
+
"percent_mapped": 68.41113655597887,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:37:11 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:37:58 2020"
|
| 44 |
+
}
|
RNA-seq/10-HS707A_S10_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
6.47085e-43 9.64514e-43 1.43536e-42 2.13264e-42 3.16359e-42 4.68542e-42 6.92823e-42 1.02282e-41 1.5076e-41 2.21857e-41 3.25963e-41 4.78154e-41 7.00281e-41 1.02396e-40 1.49485e-40 2.1788e-40 3.17061e-40 4.60653e-40 6.68206e-40 9.67724e-40 1.39926e-39 2.01999e-39 2.91142e-39 4.18955e-39 6.01915e-39 8.63391e-39 1.23647e-38 1.76794e-38 2.52381e-38 3.59707e-38 5.11856e-38 7.27196e-38 1.03148e-37 1.46075e-37 2.06536e-37 2.91554e-37 4.10913e-37 1.30388e-12 5.21551e-12 7.82327e-12 5.21551e-12 1.3027e-07 5.49332e-07 1.05822e-06 1.74203e-06 3.11459e-06 4.39161e-06 4.10579e-06 3.11119e-06 3.43345e-06 4.39871e-06 1.2201e-05 4.19266e-05 8.87867e-05 0.000132289 0.000167992 0.000193405 0.000194177 0.000169844 0.00014289 0.000132667 0.000142278 0.000164133 0.000182432 0.000189925 0.00019415 0.000197044 0.000199051 0.000208071 0.000221036 0.000227918 0.000232037 0.000244402 0.000270889 0.000306851 0.000337806 0.000363688 0.000406546 0.000477103 0.000556941 0.000598139 0.000575227 0.000525307 0.00048476 0.000465569 0.000488948 0.000558581 0.000607025 0.000584765 0.000559785 0.00058197 0.000603221 0.000595178 0.000590518 0.000616421 0.000661939 0.000711823 0.000765481 0.00082789 0.000894599 0.00093863 0.000963551 0.00099521 0.00101858 0.0010386 0.00108937 0.00114984 0.0011723 0.00116905 0.0011916 0.00125172 0.00132541 0.00139139 0.00144519 0.00150317 0.00156695 0.00163153 0.00171948 0.00182289 0.0018973 0.00194438 0.00201605 0.00213442 0.00225646 0.00235031 0.00243865 0.00253312 0.00261002 0.00266828 0.00274767 0.00285837 0.00296771 0.00306388 0.00315387 0.00324535 0.00334527 0.00345271 0.00355199 0.00360986 0.00362076 0.00362356 0.00365518 0.00372623 0.00383882 0.00398967 0.00413722 0.00419723 0.00413973 0.00408167 0.00412411 0.00421058 0.00434501 0.00459995 0.00480829 0.00476718 0.00463401 0.00464053 0.00472929 0.0047696 0.00477919 0.00481531 0.00491124 0.00506323 0.00519582 0.00528983 0.005412 0.00553579 0.0055601 0.00550198 0.00547577 0.00553872 0.00566584 0.00575611 0.00579918 0.00597268 0.00623762 0.00645525 0.00680774 0.00727087 0.00741475 0.00707646 0.00652953 0.00606259 0.00578474 0.00569094 0.00566224 0.00559614 0.00555834 0.00564975 0.00591469 0.00632117 0.00656352 0.00634624 0.00594382 0.00575998 0.00574461 0.00571111 0.00563768 0.00558274 0.00558004 0.00558119 0.00551609 0.00540972 0.00536173 0.00542518 0.00560643 0.00586294 0.00596886 0.00577538 0.00549503 0.00532104 0.00522064 0.00514937 0.00511212 0.00511592 0.00512668 0.00510972 0.00508004 0.00504507 0.00499852 0.00495682 0.00491234 0.00485614 0.00482528 0.00481893 0.00480762 0.00478239 0.00471688 0.0046185 0.00454315 0.00450401 0.0044725 0.00442772 0.00436582 0.00432223 0.0043512 0.0044418 0.00450947 0.00446854 0.00431918 0.00418901 0.00418158 0.00422302 0.00421319 0.00415551 0.00406817 0.00397457 0.00391215 0.00387804 0.00384549 0.00380098 0.00374681 0.00369408 0.00365697 0.00363009 0.00358658 0.00351538 0.00343935 0.00341868 0.00346818 0.00348268 0.00340918 0.00332949 0.00328249 0.00323995 0.00318569 0.00312757 0.00310288 0.00311974 0.00312479 0.0030842 0.00302791 0.00298188 0.0029472 0.00291921 0.00287259 0.00282949 0.00284195 0.00286418 0.0028312 0.00278016 0.00275282 0.00271566 0.00266685 0.0026649 0.00270438 0.00270286 0.00263444 0.00257039 0.00255256 0.00254683 0.00250431 0.00240521 0.00231423 0.00231429 0.00235932 0.00234221 0.00227488 0.00224419 0.00224272 0.00220859 0.00215631 0.00212408 0.00210658 0.00209287 0.00206858 0.00202393 0.00197211 0.0019245 0.00189843 0.0018983 0.00188723 0.00186332 0.00186739 0.00188067 0.00185476 0.00180115 0.00175674 0.0017373 0.00173641 0.0017185 0.00166764 0.00163654 0.00165245 0.00166078 0.00163422 0.00159112 0.00153928 0.00150937 0.00151917 0.00152777 0.00152087 0.00151332 0.00148943 0.00145569 0.00143725 0.00141929 0.00139714 0.00138028 0.00136164 0.0013394 0.00132038 0.00130719 0.00130576 0.0013201 0.00133087 0.00132011 0.00131221 0.00131392 0.00128891 0.00123628 0.00119923 0.00119776 0.0011896 0.00113856 0.0010841 0.0010692 0.00108253 0.00109329 0.0010848 0.00106592 0.00104835 0.00102962 0.00101377 0.00100766 0.00100343 0.000991741 0.000971958 0.000949665 0.000940902 0.000952789 0.00095991 0.000946886 0.000936503 0.000937222 0.000930592 0.00091009 0.000884638 0.000866634 0.000860812 0.000861133 0.000861804 0.000854427 0.000838108 0.00082834 0.000826846 0.000814149 0.000788882 0.000772498 0.000765053 0.000752566 0.000743398 0.000746444 0.000752127 0.000753062 0.000751674 0.000749287 0.000740388 0.000720571 0.000695851 0.000676003 0.000666477 0.000666737 0.000664688 0.000649095 0.000634001 0.000639683 0.000656231 0.000657673 0.000636071 0.000606066 0.000591334 0.000602855 0.00062059 0.000622517 0.000615887 0.000599947 0.000567488 0.000542633 0.000537929 0.000538831 0.000537918 0.000525958 0.000501535 0.000483596 0.000480163 0.000487585 0.0005049 0.000517779 0.00050936 0.000494258 0.000493009 0.000492844 0.000485638 0.000481357 0.000469311 0.000442976 0.000418368 0.000405955 0.000403113 0.000397471 0.000394356 0.000410474 0.000426289 0.000423358 0.000419471 0.000417017 0.000404786 0.000390931 0.000377714 0.000363674 0.000362975 0.000382303 0.000401898 0.000397683 0.000376465 0.000359046 0.000351736 0.000354859 0.000360734 0.000357794 0.000348152 0.00033634 0.000322939 0.000317769 0.000327428 0.00033951 0.000339017 0.000326361 0.000316094 0.000317662 0.000319817 0.000310134 0.000293117 0.000281772 0.000281095 0.00027762 0.000267268 0.000268748 0.00028335 0.000289695 0.000279541 0.000265822 0.00026093 0.000262569 0.000261599 0.000254909 0.000250392 0.000249544 0.000240498 0.000227315 0.000225082 0.000229456 0.000229535 0.000225209 0.000218824 0.000214419 0.000219131 0.000227434 0.00022163 0.000204295 0.000195912 0.000196252 0.000192619 0.000187746 0.000190397 0.000196682 0.000194933 0.000190009 0.000195188 0.000201806 0.000197355 0.000190463 0.000193033 0.000202078 0.000205529 0.000199703 0.000189164 0.000178607 0.000176769 0.000182264 0.000179087 0.000165944 0.000157475 0.000155607 0.000154631 0.000155462 0.000156852 0.000157217 0.000156956 0.000157386 0.000160018 0.000159453 0.000151742 0.000142294 0.000138351 0.000143584 0.000152162 0.000150667 0.000141307 0.00014001 0.000143628 0.000138744 0.000128594 0.000123092 0.00012247 0.00012026 0.000119286 0.000125517 0.00012844 0.000120715 0.000113392 0.000114916 0.000123776 0.000130833 0.000125742 0.000113859 0.000108015 0.000112432 0.00012098 0.000120594 0.000110346 0.000106216 0.000115496 0.000125773 0.000125309 0.000114696 0.000100856 9.51447e-05 9.79348e-05 9.63499e-05 9.30571e-05 0.000100171 0.000110149 0.000108044 9.66711e-05 8.83751e-05 8.73579e-05 9.10483e-05 9.47724e-05 9.5978e-05 9.83218e-05 0.00010112 9.76713e-05 8.9286e-05 8.33187e-05 8.115e-05 7.81922e-05 7.33926e-05 7.14931e-05 7.26916e-05 7.28439e-05 7.37674e-05 7.71082e-05 7.88226e-05 7.71115e-05 7.25853e-05 6.59213e-05 6.07452e-05 6.11688e-05 6.79892e-05 7.57442e-05 7.55739e-05 6.94589e-05 6.45655e-05 6.02986e-05 5.82642e-05 5.84254e-05 5.58173e-05 5.45968e-05 5.73552e-05 5.69874e-05 5.48675e-05 5.9839e-05 6.70681e-05 6.54187e-05 6.0169e-05 5.9665e-05 5.99192e-05 5.87996e-05 5.79061e-05 5.53281e-05 5.13996e-05 4.91763e-05 4.90886e-05 4.90015e-05 4.86961e-05 5.11237e-05 5.47062e-05 5.35481e-05 4.83533e-05 4.54611e-05 4.75825e-05 5.07613e-05 5.02269e-05 4.69347e-05 4.26846e-05 3.69678e-05 3.24752e-05 3.39838e-05 4.02289e-05 4.28715e-05 3.82316e-05 3.35623e-05 3.51484e-05 3.88487e-05 3.80662e-05 3.36491e-05 3.12932e-05 3.257e-05 3.53205e-05 4.02729e-05 4.63243e-05 4.82951e-05 4.59469e-05 4.33896e-05 4.32194e-05 4.32025e-05 3.89166e-05 3.34456e-05 3.12123e-05 2.99114e-05 2.94101e-05 3.16235e-05 3.4219e-05 3.52413e-05 3.42214e-05 3.06666e-05 2.77632e-05 2.8301e-05 3.10766e-05 3.54265e-05 3.91485e-05 3.8038e-05 3.33582e-05 2.97469e-05 2.80903e-05 2.8001e-05 3.06609e-05 3.45973e-05 3.47724e-05 2.98096e-05 2.46358e-05 2.40039e-05 2.60034e-05 2.57453e-05 2.45695e-05 2.52988e-05 2.7228e-05 2.91786e-05 2.85604e-05 2.61867e-05 2.54133e-05 2.67377e-05 3.07145e-05 3.3533e-05 3.05841e-05 2.63997e-05 2.50748e-05 2.50212e-05 2.48689e-05 2.36126e-05 2.22937e-05 2.23707e-05 2.23718e-05 2.26018e-05 2.45517e-05 2.55882e-05 2.25591e-05 1.85663e-05 1.88302e-05 2.14775e-05 2.24612e-05 2.28782e-05 2.33731e-05 2.2709e-05 2.17462e-05 2.15001e-05 2.13697e-05 2.08546e-05 2.00579e-05 1.89567e-05 1.7059e-05 1.46328e-05 1.43224e-05 1.72589e-05 2.02833e-05 2.01272e-05 1.69852e-05 1.36125e-05 1.27726e-05 1.55901e-05 1.89418e-05 1.84244e-05 1.58642e-05 1.56773e-05 1.76283e-05 1.92802e-05 2.03338e-05 2.10807e-05 1.99207e-05 1.83517e-05 2.069e-05 2.32051e-05 1.94129e-05 1.29531e-05 1.0743e-05 1.26894e-05 1.477e-05 1.57254e-05 1.62755e-05 1.66013e-05 1.73851e-05 1.81757e-05 1.76455e-05 1.58954e-05 1.30162e-05 1.02995e-05 1.06601e-05 1.344e-05 1.53483e-05 1.57712e-05 1.5573e-05 1.54796e-05 1.68061e-05 1.8829e-05 1.8572e-05 1.57695e-05 1.31253e-05 1.26047e-05 1.30602e-05 1.17792e-05 9.78311e-06 1.05858e-05 1.429e-05 1.66394e-05 1.43606e-05 1.02709e-05 8.32381e-06 8.29691e-06 8.97625e-06 9.07564e-06 7.51368e-06 6.38868e-06 7.36606e-06 7.68963e-06 6.24673e-06 6.98775e-06 1.06465e-05 1.3261e-05 1.3704e-05 1.26448e-05 1.07431e-05 9.80853e-06 9.28759e-06 7.9211e-06 8.14715e-06 1.08312e-05 1.18354e-05 9.76006e-06 7.79205e-06 7.15653e-06 7.99298e-06 1.05002e-05 1.18732e-05 1.04745e-05 8.78944e-06 8.07651e-06 7.95952e-06 9.04903e-06 1.02843e-05 9.76609e-06 9.16277e-06 1.11656e-05 1.40595e-05 1.42315e-05 1.14651e-05 8.03708e-06 6.09636e-06 6.78968e-06 8.85563e-06 9.5389e-06 9.88596e-06 1.31434e-05 1.60679e-05 1.49864e-05 1.43525e-05 1.4838e-05 1.1511e-05 7.22341e-06 6.43314e-06 6.55118e-06 6.32625e-06 7.81908e-06 9.39777e-06 8.13208e-06 6.06255e-06 6.2789e-06 7.53547e-06 7.48019e-06 6.47578e-06 6.21747e-06 6.56532e-06 6.05087e-06 4.74952e-06 4.18303e-06 5.17013e-06 5.99122e-06 4.93825e-06 4.20494e-06 5.84166e-06 7.36834e-06 7.00514e-06 6.47175e-06 5.90179e-06 5.36498e-06 6.97049e-06 8.79543e-06 7.65132e-06 5.68695e-06 5.30619e-06 5.40404e-06 4.84909e-06 4.31518e-06 4.26632e-06 3.59063e-06 2.10383e-06 1.47751e-06 2.61833e-06 4.37343e-06 5.31856e-06 5.45229e-06 5.04754e-06 4.03645e-06 2.75179e-06 1.96422e-06 2.4942e-06 4.11409e-06 5.89583e-06 7.55172e-06 8.20198e-06 6.3704e-06 3.30996e-06 2.20091e-06 3.36013e-06 4.48697e-06 4.51184e-06 4.08241e-06 3.68218e-06 4.10312e-06 6.17549e-06 7.50796e-06 6.13849e-06 4.95975e-06 5.60073e-06 6.46781e-06 7.22688e-06 7.20032e-06 5.06194e-06 2.43525e-06 1.52409e-06 2.03044e-06 3.20166e-06 4.28822e-06 4.07017e-06 2.85494e-06 2.32993e-06 3.16186e-06 4.266e-06 4.20127e-06 3.26912e-06 3.1516e-06 4.26884e-06 5.58919e-06 6.01042e-06 4.73379e-06 2.46848e-06 1.45621e-06 2.64635e-06 4.05046e-06 3.94954e-06 3.51799e-06 3.22325e-06 2.48104e-06 2.68595e-06 4.3468e-06 5.38407e-06 4.46624e-06 2.79206e-06 2.21242e-06 2.72657e-06 2.9566e-06 2.52045e-06 2.5725e-06 3.59753e-06 4.41953e-06 4.01123e-06 2.77535e-06 1.84218e-06 1.60018e-06 1.73652e-06 1.87357e-06 1.86389e-06 2.36647e-06 3.55344e-06 4.12045e-06 3.45442e-06 2.50558e-06 2.28023e-06 3.00719e-06 3.88983e-06 4.24245e-06 4.32099e-06 3.79375e-06 2.3631e-06 1.71994e-06 3.06255e-06 4.33572e-06 3.85106e-06 3.11498e-06 3.20248e-06 3.15451e-06 2.34668e-06 1.3505e-06 8.77665e-07 9.34649e-07 1.23189e-06 1.69436e-06 2.01414e-06 1.72389e-06 1.22159e-06 1.18457e-06 1.46894e-06 1.6588e-06 1.73614e-06 2.09799e-06 2.77084e-06 3.19171e-06 3.25957e-06 2.89582e-06 1.82601e-06 8.49631e-07 8.55962e-07 1.43733e-06 1.66603e-06 1.55487e-06 2.12956e-06 3.12096e-06 3.24687e-06 3.06542e-06 3.18137e-06 2.48852e-06 1.14825e-06 4.93577e-07 4.48333e-07 6.73553e-07 1.60662e-06 2.70055e-06 7.14187e-05 0.000276564 0.000412949
|
| 2 |
+
|
RNA-seq/10-HS707A_S10_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,53 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:37:11.538] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:37:11.626] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:37:11.627] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:37:19.362] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:37:19.362] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:37:41.677] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
|
| 12 |
+
[2020-11-04 12:37:41.680] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
|
| 13 |
+
[2020-11-04 12:37:41.699] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
|
| 14 |
+
[2020-11-04 12:37:41.718] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
|
| 15 |
+
[2020-11-04 12:37:41.720] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
|
| 16 |
+
[2020-11-04 12:37:41.720] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
|
| 17 |
+
[2020-11-04 12:37:41.727] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
|
| 18 |
+
[2020-11-04 12:37:41.728] [jointLog] [info] Thread saw mini-batch with a maximum of 2.80% zero probability fragments
|
| 19 |
+
[2020-11-04 12:37:41.761] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
|
| 20 |
+
[2020-11-04 12:37:41.769] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
|
| 21 |
+
[2020-11-04 12:37:41.770] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
|
| 22 |
+
[2020-11-04 12:37:41.782] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
|
| 23 |
+
[2020-11-04 12:37:42.105] [jointLog] [info] Computed 431,642 rich equivalence classes for further processing
|
| 24 |
+
[2020-11-04 12:37:42.105] [jointLog] [info] Counted 6,514,484 total reads in the equivalence classes
|
| 25 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] Number of mappings discarded because of alignment score : 911,361
|
| 26 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 150,183
|
| 27 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 28 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 42,813
|
| 29 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] Mapping rate = 68.4111%
|
| 30 |
+
|
| 31 |
+
[2020-11-04 12:37:42.124] [jointLog] [info] finished quantifyLibrary()
|
| 32 |
+
[2020-11-04 12:37:42.126] [jointLog] [info] Starting optimizer
|
| 33 |
+
[2020-11-04 12:37:42.106] [fileLog] [info]
|
| 34 |
+
At end of round 0
|
| 35 |
+
==================
|
| 36 |
+
Observed 9522549 total fragments (9522549 in most recent round)
|
| 37 |
+
|
| 38 |
+
[2020-11-04 12:37:42.290] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:37:42.306] [jointLog] [info] iteration = 0 | max rel diff. = 2469.37
|
| 40 |
+
[2020-11-04 12:37:43.738] [jointLog] [info] iteration = 100 | max rel diff. = 18.209
|
| 41 |
+
[2020-11-04 12:37:45.304] [jointLog] [info] iteration = 200 | max rel diff. = 16.1287
|
| 42 |
+
[2020-11-04 12:37:46.853] [jointLog] [info] iteration = 300 | max rel diff. = 0.624372
|
| 43 |
+
[2020-11-04 12:37:48.350] [jointLog] [info] iteration = 400 | max rel diff. = 0.125045
|
| 44 |
+
[2020-11-04 12:37:49.902] [jointLog] [info] iteration = 500 | max rel diff. = 0.195984
|
| 45 |
+
[2020-11-04 12:37:51.415] [jointLog] [info] iteration = 600 | max rel diff. = 0.221783
|
| 46 |
+
[2020-11-04 12:37:52.983] [jointLog] [info] iteration = 700 | max rel diff. = 3.46601
|
| 47 |
+
[2020-11-04 12:37:54.501] [jointLog] [info] iteration = 800 | max rel diff. = 0.144948
|
| 48 |
+
[2020-11-04 12:37:56.022] [jointLog] [info] iteration = 900 | max rel diff. = 0.0269093
|
| 49 |
+
[2020-11-04 12:37:57.537] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0618778
|
| 50 |
+
[2020-11-04 12:37:57.788] [jointLog] [info] iteration = 1,018 | max rel diff. = 0.00618339
|
| 51 |
+
[2020-11-04 12:37:57.806] [jointLog] [info] Finished optimizer
|
| 52 |
+
[2020-11-04 12:37:57.806] [jointLog] [info] writing output
|
| 53 |
+
|
RNA-seq/11-MCF7_S11_L001_R1_001.fastq.gz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:af1b259c7188a618babb927dff54c7c293850123a0a9b98cca3d0980bb9c7a67
|
| 3 |
+
size 604003998
|
RNA-seq/11-MCF7_S11_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/11-MCF7_S11_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 1035044,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 37521363,
|
| 35 |
+
"num_mapped": 19377956,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 128395,
|
| 38 |
+
"num_fragments_filtered_vm": 839900,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 7473246,
|
| 40 |
+
"percent_mapped": 51.645128136736399,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:38:00 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:40:36 2020"
|
| 44 |
+
}
|
RNA-seq/11-MCF7_S11_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"11-MCF7_S11_L001_R1_001.fastq.gz",
|
| 8 |
+
"11-MCF7_S11_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"11-MCF7_S11_L001_R2_001.fastq.gz",
|
| 12 |
+
"11-MCF7_S11_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "11-MCF7_S11_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/11-MCF7_S11_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
2.22295e-44 3.31343e-44 4.93095e-44 7.32635e-44 1.0868e-43 1.6096e-43 2.38009e-43 3.51375e-43 5.17911e-43 7.62156e-43 1.11979e-42 1.64262e-42 2.40571e-42 3.51765e-42 5.13532e-42 7.48494e-42 1.08922e-41 1.5825e-41 2.29552e-41 3.32447e-41 4.80694e-41 6.93937e-41 1.00018e-40 1.43926e-40 2.06779e-40 2.96605e-40 4.24773e-40 6.07351e-40 8.67018e-40 1.23572e-39 1.75841e-39 2.49818e-39 3.54351e-39 5.0182e-39 7.09525e-39 1.0016e-38 1.04934e-10 1.82253e-07 7.27963e-07 1.09154e-06 7.78046e-07 3.84219e-07 3.05866e-07 2.1944e-07 1.06113e-07 2.55035e-07 7.99129e-07 1.54872e-06 2.7429e-06 4.72212e-06 6.59726e-06 1.87493e-05 6.05712e-05 0.000116809 0.000153821 0.000182973 0.00021717 0.000222673 0.00018853 0.000152594 0.000140102 0.000144854 0.00015092 0.00015239 0.000155665 0.000161669 0.000166441 0.000174385 0.000193188 0.000212271 0.000216803 0.000216671 0.000220135 0.000233268 0.000271247 0.000314837 0.000338735 0.000364677 0.000419394 0.000490292 0.000534017 0.000530336 0.000498451 0.000459009 0.000434969 0.000447743 0.000493244 0.000529138 0.000530848 0.000541193 0.00057414 0.000587361 0.000577583 0.000582526 0.000617826 0.000660021 0.000689191 0.000715642 0.000757221 0.000821089 0.000886216 0.000927037 0.000947093 0.000949127 0.000947147 0.000978631 0.00104362 0.0011126 0.00117247 0.00121489 0.00124613 0.00130687 0.00140981 0.00149476 0.00154178 0.00160377 0.00167923 0.00174874 0.00183275 0.00191739 0.00198151 0.00204516 0.00212483 0.00221485 0.00230797 0.00239633 0.00247892 0.00257654 0.00270411 0.00284818 0.00296817 0.00303037 0.00308173 0.00318018 0.00328279 0.00337403 0.00352259 0.00370632 0.0038335 0.00388883 0.00388993 0.00387988 0.00395281 0.00410831 0.00423551 0.00431947 0.00443073 0.00451322 0.00450023 0.00448271 0.00451899 0.00464096 0.00488805 0.00506188 0.00499863 0.00488756 0.00488802 0.00497171 0.00509845 0.00519339 0.00521961 0.00525943 0.00536308 0.00550923 0.0057139 0.00592851 0.00601341 0.00596389 0.00590417 0.00590597 0.00594631 0.00600157 0.00607348 0.00617723 0.00639497 0.00666244 0.00688606 0.00726193 0.00773913 0.00786926 0.00752309 0.00697925 0.00646746 0.00607244 0.00585083 0.00580305 0.00585602 0.00593864 0.00604291 0.00625765 0.00662235 0.00681862 0.00653 0.00605098 0.00578771 0.00572279 0.0057395 0.00580999 0.00589454 0.00591359 0.00583195 0.00573918 0.00570325 0.00567062 0.00562521 0.00568914 0.00590943 0.00601993 0.00581061 0.00551367 0.00538648 0.00537984 0.00537334 0.00533328 0.00527654 0.00523207 0.00520283 0.00516557 0.00509562 0.00500125 0.00492585 0.00486288 0.00480042 0.00477896 0.00476502 0.0046943 0.00462315 0.00461781 0.00463321 0.00462477 0.00458264 0.00448103 0.0043688 0.0043353 0.00435765 0.00436985 0.00437946 0.0043916 0.00433847 0.00421152 0.00411999 0.00409687 0.00407096 0.00402772 0.00399121 0.00394742 0.00388231 0.00381827 0.00376124 0.00369948 0.00365761 0.00365483 0.00367183 0.00366354 0.00359812 0.00350925 0.00344247 0.00340305 0.00340197 0.00344061 0.00344338 0.00335468 0.00325103 0.00319782 0.00315959 0.00311472 0.00308252 0.00307176 0.00305041 0.00299223 0.00293238 0.00288762 0.00283973 0.0028121 0.00282075 0.00279983 0.00271463 0.00264639 0.00263595 0.00263552 0.00261878 0.00259302 0.00256876 0.00254577 0.00255847 0.0026412 0.00269318 0.00262929 0.00255842 0.0025558 0.00253145 0.00243117 0.00230953 0.00222707 0.0022011 0.00220061 0.0021613 0.0020724 0.00200646 0.00199152 0.00199716 0.00201368 0.00201253 0.00198471 0.00196435 0.00195663 0.00195876 0.00195051 0.00189809 0.00183373 0.00180567 0.00179025 0.00176321 0.00174863 0.00173643 0.00170401 0.00167629 0.00165354 0.0016097 0.00156809 0.00156015 0.00156728 0.00155288 0.00150479 0.00145198 0.00143076 0.00142705 0.001412 0.00139895 0.00140689 0.00143011 0.00144978 0.00144714 0.00142266 0.00138577 0.00134029 0.00129745 0.00127878 0.00129043 0.00129743 0.00127233 0.00123544 0.0012044 0.00118073 0.00116644 0.0011561 0.00114553 0.00113264 0.00112773 0.0011399 0.001136 0.00111507 0.00112129 0.00112471 0.00108551 0.00104001 0.00102436 0.00103853 0.00104913 0.0010331 0.00101643 0.00100976 0.000986945 0.000941291 0.000908547 0.000914888 0.000939907 0.000955306 0.000943354 0.000910492 0.000884503 0.000860106 0.000823721 0.000797282 0.000794891 0.000808518 0.00083177 0.000842346 0.000815226 0.000782276 0.00078593 0.000798866 0.000782639 0.000750186 0.000735512 0.000749029 0.000762005 0.00074677 0.000707245 0.000663904 0.000646154 0.00065565 0.000650229 0.000626072 0.000628219 0.000647096 0.000639447 0.000615106 0.000595768 0.000584954 0.000586872 0.000592219 0.000593002 0.000592544 0.000588826 0.000580339 0.000570507 0.000569562 0.000582443 0.000586238 0.00056051 0.000525693 0.000507048 0.000498052 0.000497037 0.000508039 0.000509815 0.000501747 0.000510803 0.000530601 0.000526797 0.000492149 0.000458068 0.000452136 0.000468996 0.000480094 0.000467112 0.000447 0.000438807 0.000435625 0.000438638 0.000455611 0.000467741 0.000454301 0.000426449 0.000411044 0.00041226 0.000412825 0.000408026 0.000406025 0.00040435 0.000398137 0.000390624 0.00037947 0.000367765 0.00036805 0.000377481 0.000379281 0.000363384 0.0003395 0.000327159 0.000327921 0.000331922 0.000336381 0.000334947 0.000325447 0.000316796 0.000311416 0.000311178 0.000316661 0.000316803 0.000310385 0.000306045 0.000303224 0.000297322 0.000284183 0.000270166 0.000272929 0.000287258 0.000284351 0.00026136 0.000244145 0.000244213 0.000254879 0.000268253 0.000271339 0.000256303 0.000241476 0.000245978 0.000254588 0.000248307 0.000239158 0.000238628 0.000239969 0.000241444 0.000243074 0.000241361 0.000238516 0.000232786 0.000219815 0.000211902 0.000221604 0.000233838 0.00023232 0.000224008 0.000216546 0.000212531 0.000213434 0.000212459 0.00020481 0.00019511 0.000191061 0.000194194 0.000195577 0.000190606 0.000185774 0.000184146 0.000184108 0.000182943 0.000175769 0.000166455 0.000164662 0.000171166 0.000181459 0.000190003 0.000187107 0.000171125 0.000155362 0.000146849 0.00014435 0.000148393 0.000150342 0.000144729 0.000140184 0.000138851 0.000139457 0.000147203 0.000159105 0.000163229 0.000158769 0.000156736 0.000156852 0.000151511 0.000144174 0.000139603 0.000137147 0.000135773 0.000132543 0.000125057 0.000117371 0.000116438 0.000124747 0.000138469 0.000146131 0.000138407 0.000124776 0.000121741 0.000128358 0.000128853 0.00011613 0.00010448 0.000105127 0.000106815 0.000102251 0.000100605 0.000105047 0.000106603 9.96945e-05 9.0438e-05 8.74961e-05 8.9072e-05 8.88187e-05 8.84481e-05 8.93233e-05 8.83513e-05 8.74043e-05 9.06654e-05 9.49475e-05 9.11483e-05 8.20494e-05 7.93225e-05 7.93992e-05 7.53231e-05 7.46672e-05 8.09036e-05 8.53321e-05 8.39921e-05 7.91878e-05 7.19336e-05 6.76542e-05 7.13059e-05 7.64831e-05 7.61689e-05 7.31649e-05 7.41297e-05 8.20068e-05 9.13004e-05 9.22001e-05 8.57367e-05 7.92859e-05 7.23374e-05 6.64889e-05 6.5515e-05 6.45296e-05 6.24742e-05 6.32345e-05 6.31123e-05 6.15946e-05 6.45673e-05 6.94208e-05 6.92811e-05 6.60487e-05 6.50254e-05 6.60864e-05 6.68833e-05 6.55647e-05 6.22246e-05 6.08162e-05 6.32891e-05 6.38123e-05 5.67766e-05 4.81574e-05 4.58926e-05 4.64515e-05 4.55175e-05 4.60205e-05 4.79097e-05 5.00896e-05 5.70201e-05 6.58377e-05 6.60244e-05 5.90034e-05 5.50419e-05 5.41167e-05 4.94812e-05 4.24584e-05 3.9152e-05 4.05172e-05 4.29368e-05 4.50207e-05 4.68281e-05 4.54914e-05 4.15521e-05 4.06119e-05 4.34184e-05 4.38327e-05 3.96715e-05 3.68347e-05 3.82487e-05 4.16638e-05 4.6171e-05 4.89277e-05 4.71877e-05 4.47172e-05 4.55131e-05 4.75509e-05 4.69432e-05 4.37194e-05 4.13401e-05 4.21427e-05 4.47425e-05 4.51399e-05 4.12622e-05 3.78621e-05 3.95924e-05 4.18775e-05 4.05853e-05 3.82344e-05 3.57196e-05 3.16113e-05 2.86134e-05 3.14079e-05 3.63029e-05 3.61131e-05 3.33245e-05 3.25313e-05 3.20729e-05 3.1381e-05 3.25688e-05 3.47552e-05 3.53745e-05 3.4446e-05 3.3282e-05 3.26012e-05 3.27052e-05 3.33413e-05 3.3772e-05 3.34294e-05 3.40031e-05 3.59251e-05 3.55876e-05 3.33511e-05 3.32595e-05 3.3963e-05 3.1757e-05 2.89721e-05 3.06161e-05 3.37766e-05 3.10162e-05 2.55644e-05 2.58291e-05 2.81499e-05 2.52358e-05 2.05698e-05 1.98842e-05 2.17007e-05 2.26195e-05 2.2222e-05 2.23566e-05 2.59824e-05 3.189e-05 3.47713e-05 3.36731e-05 2.99527e-05 2.48758e-05 2.13854e-05 1.92783e-05 1.77976e-05 1.86514e-05 1.98823e-05 1.83668e-05 1.71901e-05 1.96663e-05 2.13646e-05 1.86026e-05 1.59372e-05 1.69114e-05 1.89549e-05 1.92467e-05 1.76157e-05 1.59593e-05 1.5332e-05 1.56762e-05 1.70537e-05 1.71562e-05 1.54442e-05 1.61509e-05 1.98543e-05 2.19937e-05 2.30098e-05 2.63782e-05 2.81908e-05 2.47171e-05 2.02586e-05 1.86263e-05 1.90949e-05 1.96891e-05 1.93269e-05 1.80107e-05 1.60097e-05 1.47223e-05 1.57112e-05 1.82243e-05 2.02515e-05 2.06708e-05 2.1188e-05 2.43296e-05 2.67874e-05 2.37739e-05 1.85272e-05 1.64132e-05 1.7507e-05 1.98143e-05 2.07775e-05 1.86198e-05 1.47271e-05 1.15234e-05 1.07355e-05 1.23692e-05 1.50455e-05 1.69497e-05 1.68999e-05 1.65957e-05 1.75595e-05 1.86209e-05 1.78748e-05 1.47622e-05 1.27746e-05 1.57546e-05 2.17354e-05 2.60665e-05 2.64474e-05 2.31989e-05 1.92021e-05 1.74566e-05 1.78687e-05 1.94309e-05 2.13288e-05 2.10114e-05 1.67403e-05 1.19905e-05 1.13325e-05 1.35811e-05 1.4533e-05 1.2162e-05 8.61393e-06 8.71517e-06 1.36434e-05 1.91188e-05 2.02387e-05 1.62201e-05 1.07984e-05 7.45948e-06 7.81343e-06 1.14691e-05 1.42084e-05 1.34344e-05 1.15253e-05 1.06427e-05 1.08102e-05 1.08933e-05 9.85191e-06 8.34019e-06 7.80688e-06 8.32987e-06 8.58108e-06 8.52464e-06 9.28409e-06 1.02601e-05 1.01115e-05 9.46318e-06 9.78743e-06 1.0624e-05 1.08083e-05 1.03272e-05 9.10613e-06 7.3291e-06 6.62977e-06 8.4638e-06 1.08067e-05 9.93274e-06 6.92639e-06 6.09778e-06 7.37282e-06 8.43058e-06 9.97164e-06 1.16893e-05 1.14074e-05 9.63257e-06 8.42613e-06 8.4852e-06 9.31039e-06 9.92999e-06 8.84522e-06 6.32558e-06 4.8186e-06 4.63444e-06 4.66645e-06 5.41917e-06 6.75691e-06 7.32104e-06 6.8051e-06 6.17476e-06 7.00211e-06 9.19011e-06 9.71503e-06 7.81975e-06 7.27305e-06 8.86205e-06 9.18187e-06 8.04757e-06 8.24112e-06 1.04033e-05 1.20636e-05 1.08714e-05 7.95951e-06 6.2484e-06 6.38131e-06 6.20558e-06 4.57807e-06 3.76927e-06 5.30014e-06 6.75887e-06 7.41523e-06 9.50254e-06 1.13448e-05 1.03698e-05 8.59676e-06 7.91237e-06 7.66906e-06 7.35657e-06 7.0245e-06 6.65864e-06 6.71432e-06 6.79787e-06 5.40308e-06 3.8502e-06 4.87458e-06 7.56197e-06 9.1393e-06 8.47591e-06 6.60611e-06 6.57449e-06 8.97226e-06 1.04667e-05 1.11472e-05 1.2393e-05 1.16571e-05 9.74885e-06 9.49373e-06 9.04522e-06 7.68065e-06 6.81473e-06 6.28297e-06 6.76146e-06 8.2109e-06 8.41099e-06 6.64819e-06 4.18932e-06 2.55614e-06 2.57142e-06 3.88473e-06 5.69009e-06 7.03586e-06 6.87483e-06 5.40714e-06 4.37062e-06 4.3467e-06 3.91273e-06 4.16869e-06 7.97382e-06 1.20872e-05 1.13022e-05 8.20129e-06 6.95532e-06 6.09243e-06 4.08984e-06 2.73935e-06 3.51728e-06 4.9854e-06 4.86285e-06 3.59862e-06 3.02135e-06 3.14946e-06 3.08981e-06 2.65987e-06 2.19726e-06 2.38076e-06 3.51074e-06 5.11006e-06 6.67752e-06 7.53106e-06 7.05132e-06 5.71857e-06 4.90953e-06 5.59816e-06 6.83699e-06 6.86241e-06 5.92083e-06 5.05221e-06 4.25568e-06 4.00466e-06 4.67115e-06 5.40195e-06 5.30296e-06 4.37605e-06 3.55101e-06 3.37733e-06 3.82202e-06 4.49485e-06 4.40773e-06 3.71469e-06 3.56215e-06 3.95867e-06 4.29967e-06 4.48252e-06 4.71891e-06 5.14175e-06 5.67507e-06 6.65271e-06 7.93605e-06 8.04247e-06 6.45448e-06 4.38108e-06 3.20153e-06 3.41109e-06 4.11197e-06 4.96062e-06 6.94977e-06 8.66241e-06 7.43808e-06 5.03506e-06 4.54278e-06 5.10099e-06 5.44653e-06 6.17579e-06 6.50041e-06 5.12274e-06 3.09641e-06 2.10462e-06 1.99884e-06 1.84891e-06 1.82473e-06 2.64186e-06 4.22456e-06 5.34443e-06 5.32163e-06 5.61463e-06 6.66056e-06 6.16847e-06 3.77745e-06 1.98355e-06 2.15676e-06 3.80079e-06 5.19614e-06 4.96477e-06 4.46419e-06 5.62764e-06 0.000119002 0.000453792 0.000674796
|
| 2 |
+
|
RNA-seq/11-MCF7_S11_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 11-MCF7_S11_L001_R1_001.fastq.gz, 11-MCF7_S11_L001_R2_001.fastq.gz], [ 11-MCF7_S11_L002_R1_001.fastq.gz, 11-MCF7_S11_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 19377956,
|
| 6 |
+
"num_assigned_fragments": 19377956,
|
| 7 |
+
"num_frags_with_consistent_mappings": 16117687,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 3260269,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 16117687,
|
| 15 |
+
"SF": 1283082,
|
| 16 |
+
"SR": 1977187,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/11-MCF7_S11_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,56 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:38:00.187] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:38:00.268] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:38:00.270] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:38:08.080] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:38:08.080] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:39:36.271] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
|
| 12 |
+
[2020-11-04 12:39:36.273] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
|
| 13 |
+
[2020-11-04 12:39:36.284] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
|
| 14 |
+
[2020-11-04 12:39:36.286] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
|
| 15 |
+
[2020-11-04 12:39:36.300] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
|
| 16 |
+
[2020-11-04 12:39:36.319] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments
|
| 17 |
+
[2020-11-04 12:39:36.329] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
|
| 18 |
+
[2020-11-04 12:39:36.350] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
|
| 19 |
+
[2020-11-04 12:39:36.381] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
|
| 20 |
+
[2020-11-04 12:39:36.385] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments
|
| 21 |
+
[2020-11-04 12:39:36.386] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
|
| 22 |
+
[2020-11-04 12:39:36.402] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
|
| 23 |
+
[2020-11-04 12:39:37.187] [fileLog] [info]
|
| 24 |
+
At end of round 0
|
| 25 |
+
==================
|
| 26 |
+
Observed 37521363 total fragments (37521363 in most recent round)
|
| 27 |
+
|
| 28 |
+
[2020-11-04 12:39:37.186] [jointLog] [info] Computed 1,035,044 rich equivalence classes for further processing
|
| 29 |
+
[2020-11-04 12:39:37.186] [jointLog] [info] Counted 19,377,956 total reads in the equivalence classes
|
| 30 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] Number of mappings discarded because of alignment score : 7,473,246
|
| 31 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 839,900
|
| 32 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 33 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 128,395
|
| 34 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] Mapping rate = 51.6451%
|
| 35 |
+
|
| 36 |
+
[2020-11-04 12:39:37.204] [jointLog] [info] finished quantifyLibrary()
|
| 37 |
+
[2020-11-04 12:39:37.207] [jointLog] [info] Starting optimizer
|
| 38 |
+
[2020-11-04 12:39:37.485] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:39:37.522] [jointLog] [info] iteration = 0 | max rel diff. = 5169.86
|
| 40 |
+
[2020-11-04 12:39:41.675] [jointLog] [info] iteration = 100 | max rel diff. = 13.9412
|
| 41 |
+
[2020-11-04 12:39:46.003] [jointLog] [info] iteration = 200 | max rel diff. = 17.6501
|
| 42 |
+
[2020-11-04 12:39:50.328] [jointLog] [info] iteration = 300 | max rel diff. = 4.0478
|
| 43 |
+
[2020-11-04 12:39:54.618] [jointLog] [info] iteration = 400 | max rel diff. = 0.998576
|
| 44 |
+
[2020-11-04 12:39:58.897] [jointLog] [info] iteration = 500 | max rel diff. = 0.121091
|
| 45 |
+
[2020-11-04 12:40:02.855] [jointLog] [info] iteration = 600 | max rel diff. = 19.9374
|
| 46 |
+
[2020-11-04 12:40:06.997] [jointLog] [info] iteration = 700 | max rel diff. = 0.122184
|
| 47 |
+
[2020-11-04 12:40:11.213] [jointLog] [info] iteration = 800 | max rel diff. = 0.0751677
|
| 48 |
+
[2020-11-04 12:40:15.356] [jointLog] [info] iteration = 900 | max rel diff. = 0.103884
|
| 49 |
+
[2020-11-04 12:40:19.519] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0995749
|
| 50 |
+
[2020-11-04 12:40:23.696] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.122126
|
| 51 |
+
[2020-11-04 12:40:27.964] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.060178
|
| 52 |
+
[2020-11-04 12:40:32.215] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.200545
|
| 53 |
+
[2020-11-04 12:40:35.969] [jointLog] [info] iteration = 1,390 | max rel diff. = 0.00245728
|
| 54 |
+
[2020-11-04 12:40:35.986] [jointLog] [info] Finished optimizer
|
| 55 |
+
[2020-11-04 12:40:35.986] [jointLog] [info] writing output
|
| 56 |
+
|
RNA-seq/12-ZR-75-1_S12_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/12-ZR-75-1_S12_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 1005989,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 36381233,
|
| 35 |
+
"num_mapped": 18407383,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 113693,
|
| 38 |
+
"num_fragments_filtered_vm": 839403,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 7520534,
|
| 40 |
+
"percent_mapped": 50.59581955344944,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:40:38 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:43:20 2020"
|
| 44 |
+
}
|
RNA-seq/12-ZR-75-1_S12_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"12-ZR-75-1_S12_L001_R1_001.fastq.gz",
|
| 8 |
+
"12-ZR-75-1_S12_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"12-ZR-75-1_S12_L001_R2_001.fastq.gz",
|
| 12 |
+
"12-ZR-75-1_S12_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "12-ZR-75-1_S12_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/12-ZR-75-1_S12_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1.71641e-44 2.5584e-44 3.80733e-44 5.65689e-44 8.39152e-44 1.24282e-43 1.83773e-43 2.71307e-43 3.99894e-43 5.88483e-43 8.64626e-43 1.26832e-42 1.85751e-42 2.71607e-42 3.96512e-42 5.77932e-42 8.41012e-42 1.22189e-41 1.77243e-41 2.56691e-41 3.71156e-41 5.35807e-41 7.72264e-41 1.11129e-40 1.5966e-40 2.29017e-40 3.27979e-40 4.68952e-40 6.69448e-40 9.54136e-40 1.35772e-39 1.92891e-39 2.73604e-39 3.87469e-39 7.97679e-17 3.19072e-16 4.78607e-16 3.19072e-16 7.97679e-17 2.88154e-08 1.15262e-07 1.73634e-07 1.19235e-07 5.03796e-08 1.36006e-07 5.23931e-07 1.40845e-06 2.73599e-06 3.77031e-06 3.79157e-06 3.98545e-06 1.39113e-05 4.43022e-05 8.52191e-05 0.000126689 0.000172384 0.000201655 0.000194194 0.000171443 0.00015721 0.0001518 0.000148978 0.000149515 0.000155466 0.000160061 0.000158655 0.000151539 0.000147558 0.00016118 0.000187143 0.000210426 0.000221659 0.000215092 0.0002092 0.000231777 0.000265444 0.000284785 0.000320563 0.00040285 0.00050368 0.000565289 0.000560614 0.000513854 0.00045762 0.000422631 0.000441625 0.00051261 0.000572918 0.00056856 0.00053597 0.000532518 0.000555388 0.000571334 0.000575849 0.000601914 0.000652043 0.000687598 0.000715571 0.000768195 0.000818672 0.000845591 0.000879399 0.000932353 0.000985064 0.00102573 0.00107137 0.00112749 0.00116625 0.00119792 0.00125398 0.0013192 0.00137392 0.0014158 0.00144415 0.00147419 0.0015255 0.00162269 0.00177515 0.00191476 0.00198367 0.00203562 0.00211457 0.00218878 0.00225057 0.00233936 0.00247356 0.00262813 0.00277299 0.00289092 0.00298734 0.00308641 0.00319461 0.00331078 0.00342471 0.00350763 0.00356482 0.00365193 0.0038012 0.00393668 0.00397197 0.00395921 0.00400209 0.00412688 0.00428397 0.00439958 0.00443784 0.00442183 0.00440573 0.00446287 0.00460232 0.0047271 0.00485591 0.00509249 0.0052705 0.0052053 0.00506507 0.00500529 0.00499489 0.00503879 0.00514328 0.0052919 0.00547551 0.00560936 0.00567182 0.00580871 0.00604253 0.00618998 0.00614135 0.00601569 0.00598607 0.00604317 0.00614857 0.00631477 0.00653983 0.00688466 0.0072066 0.00741516 0.00784466 0.00840501 0.00854009 0.00815892 0.00751955 0.00683331 0.00630371 0.0060403 0.00594258 0.00584969 0.00576333 0.00582056 0.00617226 0.00681575 0.00726655 0.00702587 0.00644543 0.0061011 0.00597624 0.00593383 0.00597557 0.00602589 0.00600509 0.00589717 0.0057454 0.00563433 0.00558547 0.0055633 0.005656 0.00599117 0.00626973 0.00605109 0.005544 0.00523928 0.00516994 0.00510783 0.00501306 0.00498539 0.00501241 0.00501029 0.00497455 0.00495688 0.00496705 0.00495285 0.00487869 0.00477881 0.00470963 0.00467753 0.00462346 0.00450089 0.00438094 0.00436452 0.00441571 0.00442617 0.0043818 0.00433757 0.00427955 0.00419483 0.00417839 0.00426519 0.00433281 0.00428543 0.00416158 0.00404757 0.00398693 0.00395527 0.00392646 0.00390012 0.0038266 0.00369597 0.00360412 0.00357879 0.00355781 0.00352366 0.0034911 0.0034621 0.00344944 0.00344536 0.00341499 0.00336564 0.00331945 0.00327651 0.00324975 0.00322315 0.00316216 0.00310686 0.00309033 0.0030635 0.00300488 0.0029552 0.00292717 0.00290161 0.00288595 0.00285577 0.00276991 0.00269205 0.00268663 0.00270063 0.00268616 0.00267271 0.00266064 0.0026151 0.00257919 0.00257587 0.00253145 0.00245922 0.00244281 0.00249317 0.0025795 0.00261807 0.00254217 0.00242628 0.0023592 0.00233513 0.00232103 0.00229254 0.00223609 0.00217095 0.00212832 0.00210468 0.00207774 0.00204195 0.0020014 0.00196362 0.00195145 0.00196713 0.00196487 0.00192254 0.00186593 0.00182749 0.00183706 0.0018668 0.00183936 0.00175688 0.00169025 0.00166065 0.00164252 0.0016356 0.00165393 0.00166378 0.00162508 0.00157034 0.00154221 0.00151789 0.00148146 0.00145839 0.00145016 0.00144496 0.00144185 0.00143349 0.00142066 0.00141426 0.00140018 0.00136207 0.00132726 0.00131359 0.00131044 0.00131688 0.00131696 0.00129238 0.00125335 0.00121488 0.0011821 0.00115681 0.00114872 0.00115414 0.00114484 0.00110739 0.00105888 0.00103797 0.00105985 0.00108421 0.00107663 0.00105102 0.00104057 0.00105508 0.00106681 0.00104957 0.00102517 0.0010255 0.00101964 0.000977293 0.000944857 0.000954189 0.000960097 0.000924282 0.000871555 0.000843123 0.00085079 0.000872059 0.00087563 0.00086154 0.000849916 0.000851941 0.000857352 0.000843189 0.000822036 0.000821389 0.000825152 0.000806097 0.000775581 0.000761235 0.00076366 0.000771368 0.000776571 0.000757628 0.000711262 0.000675032 0.000671217 0.000681055 0.000687164 0.000688334 0.000677851 0.000659039 0.000645309 0.000627306 0.000610056 0.000618292 0.000630252 0.000620001 0.000611263 0.000612617 0.000607251 0.000603044 0.000609597 0.000611547 0.000594944 0.00057435 0.000574086 0.000583211 0.000577638 0.000568905 0.00056867 0.000562755 0.000545608 0.000525893 0.000513596 0.000512126 0.000513992 0.000508227 0.000490968 0.000472279 0.000464429 0.000461941 0.000452258 0.000447885 0.000463708 0.000477009 0.000467099 0.000447119 0.000427828 0.000408759 0.000403428 0.000419121 0.000430844 0.000420808 0.000405887 0.000404619 0.000413718 0.000417355 0.000406217 0.000388291 0.000377394 0.000373761 0.000367151 0.000360284 0.00036424 0.000369383 0.000361845 0.00035188 0.000355946 0.000366055 0.000358095 0.000337607 0.000325638 0.000315716 0.000302765 0.000299456 0.000307085 0.000313431 0.000308792 0.000295336 0.000284846 0.000281605 0.000281407 0.00028743 0.000300499 0.00030477 0.000290737 0.000274089 0.00026816 0.000263006 0.000254917 0.000256241 0.000262262 0.000261189 0.000259482 0.000260895 0.000260378 0.000258296 0.000253672 0.000246072 0.000239394 0.000228317 0.000214586 0.000214918 0.000224252 0.000229241 0.000238226 0.000249031 0.000244301 0.000224258 0.000206519 0.000205623 0.000213465 0.00021403 0.000212351 0.000216692 0.000220588 0.000220428 0.000217521 0.000209642 0.000202074 0.000201969 0.000204802 0.000203169 0.000194514 0.000186456 0.000187529 0.000190426 0.000190624 0.000194231 0.000199583 0.000203049 0.000201437 0.00019093 0.000176367 0.000163558 0.000157775 0.000163761 0.000171499 0.000167778 0.000158604 0.000155253 0.000154669 0.000153004 0.000153614 0.000154817 0.000151236 0.000140235 0.000126894 0.000122702 0.000130305 0.000139209 0.000140002 0.000136124 0.000134254 0.000133877 0.000133159 0.000132874 0.000133785 0.000132122 0.00012401 0.000114005 0.000111127 0.000117006 0.000124683 0.000131118 0.000132531 0.000124177 0.000116058 0.000116343 0.000117589 0.000113823 0.000108089 0.000107562 0.000113923 0.00011566 0.000105888 9.62286e-05 9.59687e-05 0.000100514 0.000102349 0.00010083 0.000102227 0.000108017 0.000110477 0.000106585 9.99552e-05 8.98696e-05 8.35939e-05 9.09043e-05 9.93865e-05 9.7817e-05 9.45323e-05 9.24527e-05 8.72753e-05 8.30434e-05 8.21161e-05 8.01732e-05 7.81984e-05 7.93631e-05 8.14153e-05 8.10761e-05 7.9897e-05 8.22695e-05 8.56755e-05 8.4297e-05 8.02511e-05 7.74261e-05 7.55898e-05 7.42657e-05 7.37315e-05 7.59341e-05 8.15646e-05 8.5266e-05 8.26847e-05 7.61627e-05 6.98951e-05 6.6717e-05 6.65844e-05 6.61496e-05 6.37163e-05 6.19069e-05 6.21038e-05 6.30366e-05 6.4556e-05 6.68329e-05 6.79473e-05 6.38051e-05 5.55197e-05 5.12971e-05 5.24358e-05 5.29015e-05 5.36063e-05 5.74337e-05 5.99566e-05 5.74385e-05 5.19047e-05 4.88677e-05 5.25573e-05 5.89424e-05 5.83713e-05 5.0202e-05 4.64466e-05 5.19546e-05 5.6808e-05 5.44828e-05 4.8544e-05 4.18051e-05 3.6122e-05 3.63324e-05 4.17497e-05 4.49421e-05 4.29073e-05 3.96652e-05 3.92046e-05 4.22045e-05 4.63887e-05 4.73998e-05 4.37308e-05 3.88344e-05 3.69572e-05 4.06139e-05 4.68077e-05 4.80058e-05 4.34267e-05 3.89797e-05 3.86915e-05 4.31941e-05 4.78839e-05 4.69243e-05 4.18013e-05 3.7555e-05 3.64075e-05 3.89687e-05 4.43585e-05 5.00347e-05 5.31776e-05 5.14935e-05 4.5366e-05 3.92861e-05 3.94852e-05 4.64884e-05 5.2284e-05 4.8667e-05 3.79505e-05 3.07629e-05 3.0064e-05 3.06241e-05 3.09464e-05 3.34777e-05 3.7892e-05 3.9419e-05 3.7473e-05 3.5339e-05 3.36266e-05 3.37928e-05 3.5743e-05 3.5622e-05 3.32923e-05 3.28778e-05 3.40175e-05 3.24773e-05 2.99946e-05 3.04407e-05 3.03196e-05 2.71141e-05 2.64632e-05 2.887e-05 2.94447e-05 3.08882e-05 3.40265e-05 3.35773e-05 3.00236e-05 2.72716e-05 2.69594e-05 2.90525e-05 3.14531e-05 3.26763e-05 3.35905e-05 3.2829e-05 2.82338e-05 2.25074e-05 1.97963e-05 2.1242e-05 2.39426e-05 2.50829e-05 2.72901e-05 3.16603e-05 3.3886e-05 3.10457e-05 2.49944e-05 2.09696e-05 2.1056e-05 2.27859e-05 2.43632e-05 2.52032e-05 2.57149e-05 2.48525e-05 2.07503e-05 1.74964e-05 1.9301e-05 2.15236e-05 1.98872e-05 1.72836e-05 1.57572e-05 1.51526e-05 1.71449e-05 2.10257e-05 2.37129e-05 2.62021e-05 2.81248e-05 2.55649e-05 2.12828e-05 1.94664e-05 1.85116e-05 1.7723e-05 1.73271e-05 1.76582e-05 1.98826e-05 2.20537e-05 2.21366e-05 2.05375e-05 1.7326e-05 1.43442e-05 1.55597e-05 2.03495e-05 2.25433e-05 1.88988e-05 1.3188e-05 1.1076e-05 1.29247e-05 1.49165e-05 1.64035e-05 1.74329e-05 1.58133e-05 1.34896e-05 1.44665e-05 1.8022e-05 2.03365e-05 1.86123e-05 1.39773e-05 1.10414e-05 1.20027e-05 1.34383e-05 1.32029e-05 1.52038e-05 2.10905e-05 2.45288e-05 2.13408e-05 1.66971e-05 1.59935e-05 1.74504e-05 1.70914e-05 1.57964e-05 1.58337e-05 1.55457e-05 1.45384e-05 1.42666e-05 1.43027e-05 1.51439e-05 1.69646e-05 1.74802e-05 1.59098e-05 1.50958e-05 1.76745e-05 2.04648e-05 1.80485e-05 1.26687e-05 1.05006e-05 1.01803e-05 8.00374e-06 6.74652e-06 8.43924e-06 1.00207e-05 1.08497e-05 1.31473e-05 1.51117e-05 1.35057e-05 1.01163e-05 8.35359e-06 8.45738e-06 9.02687e-06 8.49673e-06 7.29916e-06 8.72881e-06 1.3236e-05 1.70872e-05 1.78912e-05 1.68829e-05 1.58817e-05 1.45645e-05 1.37955e-05 1.54069e-05 1.76144e-05 1.82672e-05 1.7558e-05 1.58393e-05 1.4055e-05 1.34656e-05 1.37035e-05 1.372e-05 1.27254e-05 1.07623e-05 9.8433e-06 1.09564e-05 1.27585e-05 1.36557e-05 1.27314e-05 1.14264e-05 1.11417e-05 1.02583e-05 7.98666e-06 6.29695e-06 6.93342e-06 9.91471e-06 1.29337e-05 1.3565e-05 1.23112e-05 1.06324e-05 1.02395e-05 1.1783e-05 1.26463e-05 1.11963e-05 8.7784e-06 6.80362e-06 5.81018e-06 6.31668e-06 8.78353e-06 1.14963e-05 1.18445e-05 1.01312e-05 9.04485e-06 1.01525e-05 1.14391e-05 1.12099e-05 1.13919e-05 1.22066e-05 1.18319e-05 1.11525e-05 1.21598e-05 1.50236e-05 1.71252e-05 1.62817e-05 1.40493e-05 1.16382e-05 9.47187e-06 9.75363e-06 1.32261e-05 1.67076e-05 1.56856e-05 1.06591e-05 6.7442e-06 5.18826e-06 3.86706e-06 2.91052e-06 3.46487e-06 5.57807e-06 7.71077e-06 7.80328e-06 6.38182e-06 6.15982e-06 8.08594e-06 1.00382e-05 1.08507e-05 1.13137e-05 1.0442e-05 8.16403e-06 7.16796e-06 7.20629e-06 6.08866e-06 5.39129e-06 8.10296e-06 1.26897e-05 1.32947e-05 9.6219e-06 9.33045e-06 1.32108e-05 1.42857e-05 1.18113e-05 9.28306e-06 7.67806e-06 7.70983e-06 8.94547e-06 9.12423e-06 8.52059e-06 8.93441e-06 9.76479e-06 9.333e-06 7.43296e-06 5.84981e-06 6.19879e-06 7.41937e-06 7.76768e-06 7.12732e-06 6.2623e-06 6.31628e-06 7.62273e-06 8.51544e-06 7.58757e-06 6.06749e-06 6.36458e-06 8.95682e-06 1.17088e-05 1.2453e-05 1.07117e-05 7.78442e-06 5.83817e-06 4.74468e-06 3.18003e-06 2.61443e-06 4.08082e-06 5.03783e-06 4.2863e-06 3.45599e-06 3.00776e-06 3.19271e-06 5.08678e-06 7.83833e-06 8.94346e-06 7.88097e-06 6.99577e-06 7.47339e-06 8.04124e-06 7.52307e-06 6.29845e-06 6.1318e-06 7.24447e-06 7.89811e-06 7.5987e-06 7.56931e-06 8.33353e-06 8.35445e-06 6.72848e-06 4.84923e-06 3.85116e-06 3.48996e-06 4.01922e-06 5.59069e-06 6.14828e-06 4.90998e-06 4.31945e-06 5.13013e-06 5.91462e-06 6.50169e-06 6.87836e-06 6.95995e-06 7.53849e-06 7.69872e-06 6.13268e-06 4.25591e-06 3.65169e-06 3.93775e-06 4.50464e-06 5.40955e-06 6.09558e-06 6.01405e-06 5.7366e-06 5.89314e-06 5.74595e-06 4.47687e-06 3.59365e-06 3.75753e-06 3.9599e-06 4.85293e-06 5.91114e-06 6.20083e-06 7.29112e-06 8.41724e-06 7.74498e-06 6.27716e-06 4.71812e-06 3.27938e-06 2.73156e-06 3.81802e-06 6.44863e-06 8.37062e-06 7.79223e-06 5.44045e-06 3.30752e-06 0.000125353 0.000492635 0.000736153
|
| 2 |
+
|
RNA-seq/12-ZR-75-1_S12_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 12-ZR-75-1_S12_L001_R1_001.fastq.gz, 12-ZR-75-1_S12_L001_R2_001.fastq.gz], [ 12-ZR-75-1_S12_L002_R1_001.fastq.gz, 12-ZR-75-1_S12_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 18407383,
|
| 6 |
+
"num_assigned_fragments": 18407383,
|
| 7 |
+
"num_frags_with_consistent_mappings": 15267438,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 3139945,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 15267438,
|
| 15 |
+
"SF": 1246149,
|
| 16 |
+
"SR": 1893796,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/12-ZR-75-1_S12_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,58 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:40:38.919] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:40:38.997] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:40:38.999] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:40:46.849] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:40:46.849] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:42:12.304] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
|
| 12 |
+
[2020-11-04 12:42:12.356] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
|
| 13 |
+
[2020-11-04 12:42:12.364] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
|
| 14 |
+
[2020-11-04 12:42:12.369] [jointLog] [info] Thread saw mini-batch with a maximum of 4.38% zero probability fragments
|
| 15 |
+
[2020-11-04 12:42:12.376] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
|
| 16 |
+
[2020-11-04 12:42:12.385] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
|
| 17 |
+
[2020-11-04 12:42:12.391] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
|
| 18 |
+
[2020-11-04 12:42:12.395] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
|
| 19 |
+
[2020-11-04 12:42:12.399] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
|
| 20 |
+
[2020-11-04 12:42:12.414] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
|
| 21 |
+
[2020-11-04 12:42:12.420] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
|
| 22 |
+
[2020-11-04 12:42:12.434] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
|
| 23 |
+
[2020-11-04 12:42:13.352] [fileLog] [info]
|
| 24 |
+
At end of round 0
|
| 25 |
+
==================
|
| 26 |
+
Observed 36381233 total fragments (36381233 in most recent round)
|
| 27 |
+
|
| 28 |
+
[2020-11-04 12:42:13.351] [jointLog] [info] Computed 1,005,989 rich equivalence classes for further processing
|
| 29 |
+
[2020-11-04 12:42:13.351] [jointLog] [info] Counted 18,407,383 total reads in the equivalence classes
|
| 30 |
+
[2020-11-04 12:42:13.371] [jointLog] [info] Number of mappings discarded because of alignment score : 7,520,534
|
| 31 |
+
[2020-11-04 12:42:13.371] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 839,403
|
| 32 |
+
[2020-11-04 12:42:13.372] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 33 |
+
[2020-11-04 12:42:13.372] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 113,693
|
| 34 |
+
[2020-11-04 12:42:13.372] [jointLog] [info] Mapping rate = 50.5958%
|
| 35 |
+
|
| 36 |
+
[2020-11-04 12:42:13.372] [jointLog] [info] finished quantifyLibrary()
|
| 37 |
+
[2020-11-04 12:42:13.374] [jointLog] [info] Starting optimizer
|
| 38 |
+
[2020-11-04 12:42:13.717] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:42:13.758] [jointLog] [info] iteration = 0 | max rel diff. = 5083.12
|
| 40 |
+
[2020-11-04 12:42:17.842] [jointLog] [info] iteration = 100 | max rel diff. = 16.6829
|
| 41 |
+
[2020-11-04 12:42:22.103] [jointLog] [info] iteration = 200 | max rel diff. = 7.34351
|
| 42 |
+
[2020-11-04 12:42:26.341] [jointLog] [info] iteration = 300 | max rel diff. = 6.1079
|
| 43 |
+
[2020-11-04 12:42:30.520] [jointLog] [info] iteration = 400 | max rel diff. = 0.363587
|
| 44 |
+
[2020-11-04 12:42:34.672] [jointLog] [info] iteration = 500 | max rel diff. = 0.227366
|
| 45 |
+
[2020-11-04 12:42:38.825] [jointLog] [info] iteration = 600 | max rel diff. = 0.213214
|
| 46 |
+
[2020-11-04 12:42:42.989] [jointLog] [info] iteration = 700 | max rel diff. = 0.0793234
|
| 47 |
+
[2020-11-04 12:42:47.125] [jointLog] [info] iteration = 800 | max rel diff. = 3.48617
|
| 48 |
+
[2020-11-04 12:42:51.276] [jointLog] [info] iteration = 900 | max rel diff. = 0.0486687
|
| 49 |
+
[2020-11-04 12:42:55.380] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.14654
|
| 50 |
+
[2020-11-04 12:42:59.495] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.142484
|
| 51 |
+
[2020-11-04 12:43:03.560] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.100617
|
| 52 |
+
[2020-11-04 12:43:07.646] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0308427
|
| 53 |
+
[2020-11-04 12:43:11.730] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.226073
|
| 54 |
+
[2020-11-04 12:43:15.830] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0595172
|
| 55 |
+
[2020-11-04 12:43:19.560] [jointLog] [info] iteration = 1,592 | max rel diff. = 0.00136092
|
| 56 |
+
[2020-11-04 12:43:19.578] [jointLog] [info] Finished optimizer
|
| 57 |
+
[2020-11-04 12:43:19.578] [jointLog] [info] writing output
|
| 58 |
+
|
RNA-seq/13-A549_S13_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/13-A549_S13_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 424541,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 9201367,
|
| 35 |
+
"num_mapped": 4843750,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 26709,
|
| 38 |
+
"num_fragments_filtered_vm": 187755,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 1335548,
|
| 40 |
+
"percent_mapped": 52.64163466145846,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:43:22 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:44:09 2020"
|
| 44 |
+
}
|
RNA-seq/13-A549_S13_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"13-A549_S13_L001_R1_001.fastq.gz",
|
| 8 |
+
"13-A549_S13_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"13-A549_S13_L001_R2_001.fastq.gz",
|
| 12 |
+
"13-A549_S13_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "13-A549_S13_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/13-A549_S13_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 13-A549_S13_L001_R1_001.fastq.gz, 13-A549_S13_L001_R2_001.fastq.gz], [ 13-A549_S13_L002_R1_001.fastq.gz, 13-A549_S13_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 4843750,
|
| 6 |
+
"num_assigned_fragments": 4843750,
|
| 7 |
+
"num_frags_with_consistent_mappings": 4083537,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 760213,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 4083537,
|
| 15 |
+
"SF": 283258,
|
| 16 |
+
"SR": 476955,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/14-BxPC3_S14_L001_R1_001.fastq.gz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:48e3142c16c29e4834b125a6e8217cc685e53b6333b34c0f349ff628f9fad0d9
|
| 3 |
+
size 283413025
|
RNA-seq/14-BxPC3_S14_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/14-BxPC3_S14_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 614606,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 17671360,
|
| 35 |
+
"num_mapped": 10538764,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 67227,
|
| 38 |
+
"num_fragments_filtered_vm": 341322,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 2128254,
|
| 40 |
+
"percent_mapped": 59.63753780127845,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:44:11 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:45:21 2020"
|
| 44 |
+
}
|
RNA-seq/14-BxPC3_S14_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"14-BxPC3_S14_L001_R1_001.fastq.gz",
|
| 8 |
+
"14-BxPC3_S14_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"14-BxPC3_S14_L001_R2_001.fastq.gz",
|
| 12 |
+
"14-BxPC3_S14_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "14-BxPC3_S14_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/14-BxPC3_S14_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1.32506e-43 1.97508e-43 2.93925e-43 4.36711e-43 6.47825e-43 9.59457e-43 1.41873e-42 2.09449e-42 3.08718e-42 4.54308e-42 6.6749e-42 9.79139e-42 1.434e-41 2.09681e-41 3.06108e-41 4.46164e-41 6.49263e-41 9.43303e-41 1.36832e-40 1.98166e-40 2.86533e-40 4.13644e-40 5.96189e-40 8.57918e-40 1.23257e-39 1.76801e-39 2.532e-39 3.62032e-39 5.16815e-39 7.36594e-39 1.04816e-38 1.48912e-38 2.11223e-38 2.99126e-38 4.22936e-38 5.97034e-38 2.61832e-11 6.9833e-10 2.53149e-09 1.43538e-08 4.51506e-08 1.78418e-07 4.97781e-07 7.92366e-07 1.37792e-06 3.07113e-06 4.57994e-06 3.84164e-06 2.11884e-06 1.96244e-06 3.48087e-06 1.25416e-05 4.29634e-05 8.89041e-05 0.000127563 0.000155197 0.000172034 0.000170219 0.000158446 0.000149072 0.000141444 0.000138117 0.000147349 0.000166183 0.000179436 0.000179809 0.000176629 0.000183111 0.000201473 0.000219821 0.000227387 0.000228445 0.000232387 0.00024879 0.000283609 0.00031323 0.000320662 0.000343884 0.000419403 0.000518877 0.000571497 0.000559587 0.000524687 0.000488845 0.000475365 0.000510277 0.000571201 0.000607643 0.000603517 0.00059082 0.000598205 0.000622732 0.000642931 0.000653194 0.000680411 0.000735873 0.000790233 0.00083467 0.000893396 0.000952803 0.000983443 0.00100062 0.00102602 0.00106194 0.00111724 0.00119665 0.00126821 0.00130582 0.00135056 0.0014401 0.00153852 0.00160634 0.00165446 0.00169566 0.0017322 0.00180593 0.0019392 0.00206733 0.00214158 0.00218975 0.00223234 0.00227472 0.00235159 0.00246398 0.00258193 0.00271144 0.00285133 0.00298199 0.00310725 0.00324717 0.00338954 0.00349552 0.003582 0.00368921 0.00380781 0.00389826 0.00393767 0.003972 0.0040539 0.00415466 0.0042197 0.00426265 0.0043599 0.00451297 0.00464507 0.00474221 0.00479426 0.0047914 0.00482237 0.00489879 0.00494832 0.00505421 0.00526785 0.00539296 0.00532913 0.00524001 0.00524218 0.00531079 0.00540061 0.00547915 0.00553242 0.00557045 0.00562182 0.0057198 0.00588309 0.00607074 0.00619199 0.0062053 0.00615401 0.00612004 0.0061428 0.00618727 0.00622467 0.00629647 0.00645012 0.00661264 0.00675707 0.00699507 0.00722372 0.00722491 0.00703354 0.00678702 0.00654255 0.00632917 0.00617687 0.00607339 0.00598748 0.00595125 0.00600962 0.00618275 0.00646409 0.00665415 0.00651781 0.00619104 0.00595378 0.00586061 0.00585589 0.00589724 0.00595402 0.0059616 0.005841 0.00566448 0.00559478 0.00562845 0.00564836 0.00569481 0.00586509 0.00599172 0.00586147 0.00560435 0.00543998 0.00535577 0.0052645 0.00517657 0.00514453 0.00514479 0.00511995 0.00509561 0.00508564 0.00504443 0.00497241 0.00488955 0.00480851 0.00476122 0.00475793 0.00476963 0.0047435 0.00466279 0.00460155 0.00459043 0.00453438 0.00442372 0.00437487 0.00438318 0.00435738 0.00432241 0.00431038 0.00426571 0.00419066 0.0041259 0.0040648 0.00402842 0.00402655 0.00400452 0.00394429 0.00387539 0.00381389 0.00377328 0.00374734 0.00370684 0.00364902 0.00356876 0.00347559 0.00343741 0.00346356 0.00347024 0.00341228 0.00333604 0.00330923 0.00332219 0.00330001 0.00323 0.00317193 0.00313847 0.0030998 0.00306029 0.00303858 0.00303153 0.00302006 0.00299259 0.00295182 0.00290215 0.00284816 0.0027898 0.00271951 0.00263824 0.00257491 0.00256928 0.00260253 0.00260619 0.00256613 0.00252261 0.00248906 0.00244187 0.00238623 0.00238038 0.00242066 0.00240566 0.0023281 0.00229802 0.00231036 0.00226497 0.00218103 0.00214376 0.00213606 0.00210075 0.00205032 0.0020104 0.00198222 0.00196572 0.00194591 0.00190593 0.00185416 0.00181507 0.00181275 0.00183733 0.00184251 0.0018174 0.00178531 0.00174747 0.00170413 0.00166513 0.00163445 0.00162414 0.00163909 0.00166021 0.00167172 0.00166247 0.00162165 0.00156112 0.00149705 0.00143933 0.00141948 0.00144022 0.00144352 0.00141556 0.00139175 0.00137199 0.00135933 0.0013655 0.00136125 0.00133227 0.00131069 0.00130882 0.00130906 0.00130561 0.00129065 0.0012512 0.00120906 0.00119554 0.00119971 0.00119542 0.00117462 0.00114382 0.00111731 0.00110104 0.00108956 0.00108441 0.00109508 0.00110612 0.00108682 0.00104633 0.0010157 0.000996245 0.000977063 0.000959864 0.000946325 0.000938035 0.000928717 0.000908506 0.000892611 0.000888313 0.000879806 0.000870593 0.000870665 0.00086858 0.000856348 0.000847275 0.000853892 0.000871586 0.000875205 0.000844803 0.000801359 0.000772282 0.000758321 0.000753901 0.000750076 0.000736848 0.000714709 0.000700376 0.000716307 0.000740191 0.000728496 0.000697265 0.000686136 0.000690951 0.00068525 0.000664659 0.000649628 0.000645903 0.000635701 0.000620513 0.00062171 0.000637525 0.000638562 0.00061498 0.000596659 0.000604028 0.000613182 0.000594799 0.000565471 0.000558859 0.000563646 0.000550673 0.000533683 0.000538047 0.000549958 0.000548076 0.000534555 0.000519348 0.000514513 0.000521914 0.000518988 0.000493898 0.000467148 0.000454437 0.000445322 0.000432615 0.000428763 0.00043173 0.000432417 0.000440724 0.000444536 0.000425237 0.00040315 0.000397877 0.000403787 0.000404743 0.000392885 0.000382121 0.00038103 0.000379812 0.00037267 0.000361417 0.000351669 0.000353529 0.000362258 0.000356468 0.00033885 0.000334636 0.000346253 0.000357421 0.000357978 0.000347633 0.000339927 0.000344496 0.000348362 0.000337007 0.000315446 0.000301204 0.000299574 0.000296855 0.000287082 0.000281993 0.000291633 0.000308402 0.00031191 0.000297269 0.000285893 0.000287659 0.000282831 0.00026263 0.000245942 0.000247345 0.000259176 0.000264082 0.000255433 0.000242748 0.000239939 0.000249734 0.000255655 0.000243664 0.000230989 0.000238154 0.000249946 0.000244905 0.000228744 0.000217444 0.000214636 0.000212976 0.000208474 0.000201349 0.000195281 0.000200609 0.000210027 0.000201653 0.000188786 0.000197036 0.000205919 0.00019177 0.000174569 0.000172498 0.000180393 0.000190788 0.000192304 0.000185038 0.000181545 0.000177372 0.000168996 0.000166919 0.000170723 0.000171923 0.000166018 0.00015899 0.000164953 0.000174576 0.000166471 0.000151848 0.000147845 0.000143435 0.0001314 0.000126245 0.000137322 0.000153044 0.000159256 0.00015682 0.00015061 0.000142702 0.000138278 0.000138602 0.000139448 0.000138885 0.000133488 0.000121298 0.000111209 0.000114076 0.00012443 0.000124558 0.00011413 0.000108227 0.00010931 0.000111137 0.000109057 0.000102834 9.90383e-05 9.72099e-05 9.21895e-05 8.94648e-05 9.3147e-05 9.6259e-05 9.52229e-05 9.61992e-05 0.000101965 0.000105088 0.00010201 0.000101011 0.000105274 0.000107301 0.000102919 9.26348e-05 8.25038e-05 8.12463e-05 8.51903e-05 8.8036e-05 9.3882e-05 0.000102197 0.000104695 0.000102523 0.000103075 0.000103045 9.54603e-05 8.41909e-05 7.98708e-05 8.67682e-05 9.48446e-05 9.26473e-05 8.37421e-05 7.79754e-05 7.63772e-05 7.35074e-05 6.91262e-05 6.85816e-05 7.21956e-05 7.55654e-05 7.85758e-05 8.15416e-05 7.98994e-05 7.26356e-05 6.55736e-05 6.34497e-05 6.44761e-05 6.45679e-05 6.31861e-05 6.03397e-05 5.67957e-05 5.5655e-05 5.485e-05 5.0845e-05 4.69723e-05 4.70873e-05 5.08058e-05 5.48581e-05 5.82874e-05 6.0683e-05 5.68307e-05 4.94572e-05 4.69505e-05 4.72951e-05 4.62202e-05 4.35964e-05 4.08312e-05 4.28929e-05 5.18132e-05 6.11743e-05 6.36239e-05 5.97234e-05 5.343e-05 4.59038e-05 4.15168e-05 4.32692e-05 4.61626e-05 4.63459e-05 4.50442e-05 4.51477e-05 4.73491e-05 4.89265e-05 4.74309e-05 4.36647e-05 4.06568e-05 3.96536e-05 4.02077e-05 4.13168e-05 4.0493e-05 3.64149e-05 3.20807e-05 3.20306e-05 3.48479e-05 3.57274e-05 3.64624e-05 3.95773e-05 4.23169e-05 4.39095e-05 4.2944e-05 3.71e-05 3.1458e-05 3.05884e-05 3.24567e-05 3.48392e-05 3.58485e-05 3.52467e-05 3.37659e-05 3.16788e-05 3.19625e-05 3.36155e-05 3.32589e-05 3.20777e-05 3.07651e-05 3.03615e-05 3.07998e-05 2.90461e-05 2.63646e-05 2.62653e-05 2.82062e-05 3.00433e-05 3.151e-05 3.18638e-05 3.03927e-05 2.93677e-05 2.96711e-05 3.0271e-05 3.11962e-05 3.13714e-05 2.99812e-05 2.83059e-05 2.70254e-05 2.51717e-05 2.26514e-05 2.21035e-05 2.51092e-05 2.77343e-05 2.55292e-05 2.11323e-05 2.03421e-05 2.35507e-05 2.65304e-05 2.67319e-05 2.45622e-05 2.08376e-05 1.64146e-05 1.29144e-05 1.15394e-05 1.25634e-05 1.57636e-05 1.91193e-05 2.05854e-05 2.02716e-05 1.84883e-05 1.58327e-05 1.36555e-05 1.27382e-05 1.35146e-05 1.57356e-05 1.69308e-05 1.5173e-05 1.22728e-05 1.04003e-05 1.09244e-05 1.37472e-05 1.43758e-05 1.22358e-05 1.28139e-05 1.55715e-05 1.72168e-05 1.81656e-05 1.72038e-05 1.37717e-05 1.09695e-05 1.09531e-05 1.27108e-05 1.34584e-05 1.39954e-05 1.80236e-05 2.12333e-05 1.84222e-05 1.54433e-05 1.52421e-05 1.43292e-05 1.41848e-05 1.56447e-05 1.55579e-05 1.42943e-05 1.56353e-05 1.97746e-05 2.12613e-05 1.80598e-05 1.49869e-05 1.40932e-05 1.32117e-05 1.19368e-05 1.12627e-05 1.1543e-05 1.35016e-05 1.67963e-05 1.83698e-05 1.65305e-05 1.36556e-05 1.2729e-05 1.39905e-05 1.59995e-05 1.69852e-05 1.54697e-05 1.17286e-05 8.17218e-06 7.55944e-06 9.40308e-06 1.09202e-05 1.15529e-05 1.17577e-05 1.11943e-05 1.0381e-05 1.00332e-05 1.00425e-05 9.94416e-06 9.03597e-06 8.16413e-06 9.36935e-06 1.1305e-05 1.12981e-05 1.02953e-05 9.60991e-06 8.33483e-06 6.51775e-06 6.08938e-06 7.54996e-06 9.46449e-06 1.09823e-05 1.15715e-05 1.13265e-05 1.17329e-05 1.2753e-05 1.25487e-05 1.06782e-05 8.76043e-06 8.70469e-06 9.55567e-06 8.2715e-06 5.40624e-06 4.34154e-06 5.74002e-06 8.05588e-06 9.71083e-06 9.50113e-06 8.3507e-06 8.10639e-06 8.2069e-06 7.94584e-06 8.76675e-06 1.03815e-05 1.03562e-05 8.56813e-06 7.4106e-06 7.43081e-06 6.82907e-06 6.28025e-06 7.30548e-06 8.08838e-06 7.57902e-06 7.43101e-06 7.6121e-06 6.87963e-06 6.875e-06 8.46615e-06 8.19314e-06 5.14462e-06 3.01538e-06 3.40039e-06 4.24175e-06 3.93278e-06 3.54104e-06 4.24504e-06 5.231e-06 5.51884e-06 5.17427e-06 4.69764e-06 4.39751e-06 4.05596e-06 4.02436e-06 4.94357e-06 5.89762e-06 6.0097e-06 5.93411e-06 6.05453e-06 5.77538e-06 4.9518e-06 4.3782e-06 4.62287e-06 5.33589e-06 5.78793e-06 5.76804e-06 5.08137e-06 3.69629e-06 2.88085e-06 3.27136e-06 3.85404e-06 3.69035e-06 3.1304e-06 3.58816e-06 5.11883e-06 6.40746e-06 6.90936e-06 5.97346e-06 3.58723e-06 1.87472e-06 1.8535e-06 2.25851e-06 2.27469e-06 2.20401e-06 2.43442e-06 2.71522e-06 2.86242e-06 3.52744e-06 4.8805e-06 6.18268e-06 6.63484e-06 5.34747e-06 2.96287e-06 1.86943e-06 2.19748e-06 2.28088e-06 2.27897e-06 2.5618e-06 2.73108e-06 3.26283e-06 4.30913e-06 5.55831e-06 6.55875e-06 5.86432e-06 3.49549e-06 1.4044e-06 5.8621e-07 8.21693e-07 1.7125e-06 3.17477e-06 4.83538e-06 5.65301e-06 5.60686e-06 5.11635e-06 3.85518e-06 2.54376e-06 1.93079e-06 1.75411e-06 2.33778e-06 3.27084e-06 3.58868e-06 3.90622e-06 4.61325e-06 4.8002e-06 4.24788e-06 3.6219e-06 3.13602e-06 2.55743e-06 2.05991e-06 2.12651e-06 2.27967e-06 1.79653e-06 1.3208e-06 1.19872e-06 8.27755e-07 3.47091e-07 2.00983e-07 3.79744e-07 1.09687e-06 2.55015e-06 3.80004e-06 3.61573e-06 2.61123e-06 2.61292e-06 3.67765e-06 3.86305e-06 2.60352e-06 1.32863e-06 9.528e-07 1.71828e-06 3.21344e-06 3.89325e-06 3.38183e-06 3.17387e-06 3.63089e-06 3.8963e-06 3.57525e-06 2.72982e-06 2.64356e-06 3.82242e-06 4.43769e-06 4.22578e-06 4.39784e-06 4.18605e-06 3.19431e-06 3.00106e-06 3.34266e-06 2.63591e-06 1.92234e-06 2.6713e-06 3.605e-06 3.18914e-06 2.11258e-06 1.50893e-06 1.40434e-06 1.78117e-06 2.40397e-06 2.2759e-06 1.57362e-06 1.62418e-06 2.0214e-06 1.54311e-06 6.95507e-07 3.85674e-07 6.16147e-07 9.69214e-07 1.18747e-06 1.25991e-06 1.02912e-06 1.04248e-06 2.15732e-06 3.26973e-06 3.02169e-06 2.2731e-06 2.00827e-06 2.3636e-06 3.12396e-06 3.14785e-06 1.98729e-06 7.78349e-07 2.57631e-07 3.59307e-07 9.39073e-07 1.38461e-06 1.2155e-06 8.16566e-07 7.09611e-07 1.09029e-06 1.55465e-06 1.59073e-06 1.44683e-06 1.44687e-06 1.31566e-06 8.7116e-07 8.3223e-07 1.79926e-06 2.77777e-06 2.58681e-06 1.67375e-06 1.00987e-06 7.4556e-07 6.51845e-07 6.72526e-07 9.37526e-07 1.53602e-06 1.87216e-06 1.42728e-06 1.02468e-06 1.4272e-06 1.99231e-06 1.80887e-06 1.17356e-06 1.00086e-06 1.17519e-06 1.25128e-06 6.14258e-05 0.000241518 0.000361103
|
| 2 |
+
|
RNA-seq/14-BxPC3_S14_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 14-BxPC3_S14_L001_R1_001.fastq.gz, 14-BxPC3_S14_L001_R2_001.fastq.gz], [ 14-BxPC3_S14_L002_R1_001.fastq.gz, 14-BxPC3_S14_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 10538764,
|
| 6 |
+
"num_assigned_fragments": 10538764,
|
| 7 |
+
"num_frags_with_consistent_mappings": 8994474,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 1544290,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 8994474,
|
| 15 |
+
"SF": 517715,
|
| 16 |
+
"SR": 1026575,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/14-BxPC3_S14_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,52 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:44:11.288] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:44:11.364] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:44:11.366] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:44:19.096] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:44:19.096] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:44:58.670] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
|
| 12 |
+
[2020-11-04 12:44:58.674] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
|
| 13 |
+
[2020-11-04 12:44:58.676] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
|
| 14 |
+
[2020-11-04 12:44:58.685] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
|
| 15 |
+
[2020-11-04 12:44:58.704] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
|
| 16 |
+
[2020-11-04 12:44:58.716] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
|
| 17 |
+
[2020-11-04 12:44:58.733] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
|
| 18 |
+
[2020-11-04 12:44:58.745] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
|
| 19 |
+
[2020-11-04 12:44:58.746] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
|
| 20 |
+
[2020-11-04 12:44:58.747] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
|
| 21 |
+
[2020-11-04 12:44:58.749] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
|
| 22 |
+
[2020-11-04 12:44:58.754] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
|
| 23 |
+
[2020-11-04 12:44:59.285] [jointLog] [info] Computed 614,606 rich equivalence classes for further processing
|
| 24 |
+
[2020-11-04 12:44:59.285] [jointLog] [info] Counted 10,538,764 total reads in the equivalence classes
|
| 25 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] Number of mappings discarded because of alignment score : 2,128,254
|
| 26 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 341,322
|
| 27 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 28 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 67,227
|
| 29 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] Mapping rate = 59.6375%
|
| 30 |
+
|
| 31 |
+
[2020-11-04 12:44:59.303] [jointLog] [info] finished quantifyLibrary()
|
| 32 |
+
[2020-11-04 12:44:59.306] [jointLog] [info] Starting optimizer
|
| 33 |
+
[2020-11-04 12:44:59.286] [fileLog] [info]
|
| 34 |
+
At end of round 0
|
| 35 |
+
==================
|
| 36 |
+
Observed 17671360 total fragments (17671360 in most recent round)
|
| 37 |
+
|
| 38 |
+
[2020-11-04 12:44:59.509] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:44:59.531] [jointLog] [info] iteration = 0 | max rel diff. = 3631.86
|
| 40 |
+
[2020-11-04 12:45:01.493] [jointLog] [info] iteration = 100 | max rel diff. = 14.927
|
| 41 |
+
[2020-11-04 12:45:03.655] [jointLog] [info] iteration = 200 | max rel diff. = 11.0617
|
| 42 |
+
[2020-11-04 12:45:05.901] [jointLog] [info] iteration = 300 | max rel diff. = 1.9949
|
| 43 |
+
[2020-11-04 12:45:07.979] [jointLog] [info] iteration = 400 | max rel diff. = 3.1444
|
| 44 |
+
[2020-11-04 12:45:10.146] [jointLog] [info] iteration = 500 | max rel diff. = 0.90122
|
| 45 |
+
[2020-11-04 12:45:12.189] [jointLog] [info] iteration = 600 | max rel diff. = 7.33963
|
| 46 |
+
[2020-11-04 12:45:14.263] [jointLog] [info] iteration = 700 | max rel diff. = 0.480069
|
| 47 |
+
[2020-11-04 12:45:16.330] [jointLog] [info] iteration = 800 | max rel diff. = 0.098915
|
| 48 |
+
[2020-11-04 12:45:18.394] [jointLog] [info] iteration = 900 | max rel diff. = 0.04559
|
| 49 |
+
[2020-11-04 12:45:20.542] [jointLog] [info] iteration = 999 | max rel diff. = 0.00828178
|
| 50 |
+
[2020-11-04 12:45:20.559] [jointLog] [info] Finished optimizer
|
| 51 |
+
[2020-11-04 12:45:20.559] [jointLog] [info] writing output
|
| 52 |
+
|
RNA-seq/15-Colo320_S15_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/15-Colo320_S15_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 1488961,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 69619954,
|
| 35 |
+
"num_mapped": 29773109,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 211511,
|
| 38 |
+
"num_fragments_filtered_vm": 1774391,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 17528289,
|
| 40 |
+
"percent_mapped": 42.76519487502103,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:45:22 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:49:47 2020"
|
| 44 |
+
}
|
RNA-seq/15-Colo320_S15_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"15-Colo320_S15_L001_R1_001.fastq.gz",
|
| 8 |
+
"15-Colo320_S15_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"15-Colo320_S15_L001_R2_001.fastq.gz",
|
| 12 |
+
"15-Colo320_S15_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "15-Colo320_S15_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/15-Colo320_S15_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1.8762e-45 2.79657e-45 4.16177e-45 6.18352e-45 9.17274e-45 1.35852e-44 2.00882e-44 2.96565e-44 4.37122e-44 6.43268e-44 9.45119e-44 1.38639e-43 2.03044e-43 2.96894e-43 4.33427e-43 6.31737e-43 9.1931e-43 1.33565e-42 1.93744e-42 2.80589e-42 4.05711e-42 5.85691e-42 8.44161e-42 1.21475e-41 1.74524e-41 2.50338e-41 3.58513e-41 5.12611e-41 7.31773e-41 1.04297e-40 1.48412e-40 2.1085e-40 2.99076e-40 4.23542e-40 5.98847e-40 8.45358e-40 1.22086e-11 4.88343e-11 7.32515e-11 9.42373e-09 2.43816e-07 9.30664e-07 1.51656e-06 1.40927e-06 1.318e-06 1.80345e-06 1.96599e-06 1.56565e-06 2.5188e-06 5.71652e-06 9.08892e-06 2.17041e-05 6.19778e-05 0.000120634 0.000177461 0.000238364 0.000286366 0.000279149 0.000233222 0.000204614 0.000205979 0.000218696 0.000232441 0.000235814 0.000220841 0.000204612 0.000210149 0.000238079 0.000271167 0.00029144 0.000295163 0.000296769 0.000308411 0.000332986 0.000379073 0.000431778 0.000468142 0.000512201 0.000584818 0.000674517 0.000754033 0.000782095 0.000741601 0.000665856 0.000620065 0.000648657 0.000735043 0.000792767 0.000768164 0.000733212 0.000747256 0.000780878 0.000802559 0.000811696 0.000833949 0.000877656 0.000915772 0.000950706 0.00101571 0.00110557 0.00118146 0.00122983 0.00126856 0.00131462 0.00136202 0.00139768 0.00144304 0.00152509 0.0016156 0.00168193 0.00175327 0.00185728 0.0019555 0.00200752 0.00203305 0.00206639 0.00212167 0.00221175 0.00231655 0.002394 0.00247844 0.00261487 0.00275052 0.00283822 0.00290815 0.0029963 0.00311481 0.00325821 0.0033872 0.00349452 0.00362979 0.00376872 0.0038545 0.00392495 0.00403089 0.00416445 0.00428225 0.00435855 0.00442326 0.00449336 0.00452217 0.00449862 0.00451028 0.00460518 0.00472674 0.00485037 0.00498994 0.00507434 0.00506454 0.00505991 0.00510129 0.00519719 0.00539271 0.00552802 0.00543883 0.0052869 0.00526445 0.00536328 0.00549615 0.0055997 0.00566768 0.00571213 0.00576098 0.00585387 0.00600921 0.00620758 0.00634861 0.00635318 0.00628578 0.00623878 0.00622955 0.00625483 0.00627114 0.00629594 0.00650292 0.006829 0.00708372 0.00742495 0.00784728 0.00792475 0.0075037 0.00690107 0.00641043 0.00605459 0.00582167 0.00574385 0.00575888 0.00580237 0.00586276 0.00598601 0.00628516 0.0065691 0.00642863 0.00597356 0.00566649 0.00562085 0.0056614 0.00566346 0.00562374 0.00557392 0.0055053 0.00543082 0.00538876 0.00536873 0.00535583 0.00542418 0.00563833 0.00579529 0.00563769 0.00530995 0.00511874 0.00508753 0.00505713 0.00497727 0.00492629 0.00492037 0.00488159 0.00480628 0.00476595 0.00475541 0.0047134 0.00462257 0.00453005 0.00449316 0.00448583 0.0044569 0.00442513 0.00439243 0.00433833 0.00429278 0.0042441 0.00415533 0.00407789 0.00404496 0.0040058 0.00395529 0.00394177 0.0039643 0.00398491 0.0039514 0.00383653 0.00372885 0.00370206 0.0036965 0.00365858 0.00357436 0.00346544 0.00341395 0.00342219 0.00340176 0.00332494 0.00324582 0.00322146 0.00324904 0.003266 0.00324309 0.00322137 0.00318917 0.00312409 0.00309843 0.0031135 0.00308522 0.00302061 0.00297134 0.00295038 0.00292497 0.00283831 0.00273307 0.00269314 0.00267342 0.0026206 0.00258945 0.00260887 0.00261851 0.00257492 0.0025047 0.00245292 0.00243458 0.00243297 0.00242534 0.00239119 0.00233695 0.00229837 0.00228904 0.00231409 0.00236437 0.00236465 0.00227571 0.00218237 0.00215139 0.00214167 0.00210718 0.00205187 0.00200393 0.00199783 0.00202551 0.00202858 0.00197433 0.0018958 0.00184313 0.00183265 0.0018512 0.00186104 0.00183026 0.00177273 0.00171191 0.00166977 0.00167575 0.00170794 0.00172361 0.00171478 0.00167261 0.00161445 0.00157876 0.0015711 0.00157647 0.00156162 0.00151289 0.00146931 0.00145373 0.00144972 0.00145336 0.0014668 0.00146691 0.00143269 0.00138424 0.00135356 0.00133297 0.00129979 0.00126413 0.00124992 0.00125583 0.00125936 0.00125339 0.00124802 0.00122821 0.00118879 0.00116685 0.00115741 0.00114092 0.0011436 0.00114652 0.00112092 0.00111011 0.00113713 0.00115518 0.001123 0.00106922 0.00104492 0.00104795 0.00104394 0.00101743 0.000989755 0.000981406 0.000984134 0.000986852 0.000979864 0.000960431 0.000935637 0.000919467 0.000929575 0.000951502 0.000948604 0.000913698 0.000869024 0.000832396 0.000821676 0.000849846 0.000877872 0.000855071 0.000797504 0.000757828 0.000753825 0.000752787 0.000733374 0.000721929 0.000729398 0.00073094 0.000723184 0.000725229 0.000724458 0.000691858 0.000650895 0.000645789 0.000664146 0.000666809 0.000648004 0.000635003 0.000637265 0.000622146 0.000590173 0.000586999 0.000609139 0.000622201 0.000625422 0.000615178 0.000591512 0.000590859 0.000605898 0.000589652 0.000558822 0.000544662 0.000533074 0.000517544 0.000511724 0.000522676 0.000538216 0.000539124 0.000532111 0.000532721 0.000527127 0.000500259 0.000466531 0.000441393 0.000430445 0.00043943 0.000452894 0.000451376 0.00044691 0.000450337 0.000449952 0.000441559 0.000436208 0.000434668 0.000424476 0.000406619 0.000396541 0.000400398 0.000409709 0.000417544 0.000423499 0.000418299 0.000390396 0.00035354 0.000335618 0.00034161 0.000354905 0.000362287 0.000363728 0.000364818 0.000363213 0.000354632 0.000345174 0.000341248 0.00033454 0.000314194 0.000291231 0.000286676 0.000303365 0.000321277 0.000323853 0.000315419 0.0003015 0.000291676 0.000292323 0.000287427 0.000276537 0.000277339 0.000283537 0.00028119 0.00027436 0.000272277 0.000277031 0.000280578 0.00027839 0.000273485 0.000265523 0.000259043 0.000260135 0.000265526 0.000265143 0.000258631 0.000259598 0.000261169 0.000246362 0.000227205 0.000221489 0.000230655 0.00024358 0.000239189 0.000223394 0.000224476 0.00023211 0.000228412 0.000229381 0.000236553 0.000233462 0.000222364 0.000213185 0.00020734 0.000201901 0.000196302 0.000196844 0.000206153 0.000210759 0.000199821 0.000182682 0.000167367 0.000155216 0.00015932 0.000179145 0.00018777 0.000176842 0.000163311 0.000154472 0.000148458 0.000149284 0.000159556 0.000171495 0.00017426 0.000170861 0.000171014 0.000170552 0.000160812 0.000146247 0.000140967 0.000149688 0.000163057 0.000170017 0.000164607 0.000155096 0.000154165 0.000156844 0.000152456 0.000144038 0.000138831 0.000132596 0.000123287 0.00012266 0.000129711 0.000127986 0.000122074 0.000126368 0.00013117 0.000127846 0.00012847 0.000137284 0.000143762 0.000142845 0.000136705 0.000129514 0.000126471 0.00012914 0.000137731 0.000146422 0.000144568 0.000133989 0.000125858 0.000123656 0.000117998 0.000108087 0.000107839 0.000113531 0.000112971 0.000115538 0.000124339 0.00012201 0.000108692 0.000101789 0.000104208 0.000107256 0.00010561 9.8745e-05 8.90888e-05 8.12099e-05 7.80947e-05 7.95447e-05 8.74102e-05 0.000101069 0.000108633 0.000100592 8.81107e-05 8.65205e-05 9.13367e-05 9.32955e-05 9.25082e-05 8.99451e-05 8.83798e-05 8.71489e-05 7.93044e-05 6.9363e-05 6.82723e-05 7.59116e-05 8.38951e-05 8.26662e-05 7.57052e-05 7.79441e-05 8.83377e-05 8.99759e-05 7.61938e-05 6.02166e-05 5.613e-05 5.89117e-05 5.94292e-05 6.25284e-05 6.96909e-05 7.07082e-05 6.55798e-05 6.34439e-05 6.58166e-05 7.35751e-05 8.30513e-05 7.91444e-05 6.23754e-05 5.09794e-05 5.05084e-05 5.63505e-05 6.61881e-05 7.31206e-05 7.22563e-05 6.88031e-05 6.61451e-05 6.42342e-05 6.43402e-05 6.37923e-05 6.05486e-05 5.86367e-05 5.92568e-05 5.83223e-05 5.57155e-05 5.6846e-05 6.23772e-05 6.62006e-05 6.63202e-05 6.48816e-05 6.13763e-05 5.5095e-05 4.92071e-05 4.78216e-05 4.94755e-05 5.03091e-05 4.98583e-05 4.85356e-05 4.72118e-05 4.89028e-05 5.38196e-05 5.69291e-05 5.71393e-05 5.64727e-05 5.22293e-05 4.69793e-05 4.77286e-05 5.13406e-05 5.00772e-05 4.30521e-05 3.76151e-05 3.97216e-05 4.51417e-05 4.87193e-05 5.04549e-05 5.19936e-05 5.54342e-05 5.82957e-05 5.49676e-05 4.60916e-05 3.77224e-05 3.33973e-05 3.2757e-05 3.51153e-05 3.83125e-05 3.90101e-05 3.84137e-05 3.95052e-05 4.20453e-05 4.41219e-05 4.25949e-05 3.74441e-05 3.47767e-05 3.76306e-05 3.99839e-05 3.82007e-05 3.7611e-05 3.82412e-05 3.51465e-05 3.2498e-05 3.41345e-05 3.61596e-05 3.47717e-05 2.83761e-05 2.16075e-05 2.14855e-05 2.59542e-05 2.84795e-05 2.85731e-05 3.03932e-05 3.26443e-05 3.01518e-05 2.51794e-05 2.29078e-05 2.27203e-05 2.17273e-05 1.93877e-05 1.9185e-05 2.50634e-05 3.31928e-05 3.52584e-05 3.15001e-05 3.18774e-05 4.31683e-05 5.57407e-05 5.34294e-05 3.95768e-05 2.97926e-05 2.70026e-05 2.66788e-05 2.747e-05 2.76265e-05 2.57567e-05 2.28051e-05 2.13407e-05 2.35029e-05 2.64599e-05 2.64369e-05 2.43169e-05 2.17094e-05 1.92264e-05 1.85454e-05 2.05154e-05 2.2743e-05 2.34283e-05 2.45881e-05 2.64651e-05 2.52003e-05 1.94582e-05 1.52521e-05 1.94589e-05 2.67947e-05 2.67479e-05 2.25142e-05 2.21328e-05 2.25915e-05 1.98893e-05 1.79677e-05 2.03172e-05 2.33078e-05 2.1872e-05 1.80099e-05 1.73923e-05 1.99282e-05 2.07415e-05 1.88284e-05 1.68009e-05 1.57029e-05 1.52002e-05 1.53821e-05 1.83649e-05 2.33259e-05 2.51381e-05 2.37836e-05 2.2469e-05 2.04292e-05 1.78543e-05 1.7844e-05 1.89244e-05 1.7914e-05 1.7814e-05 2.0802e-05 2.24204e-05 1.98235e-05 1.79061e-05 2.03657e-05 2.09204e-05 1.63882e-05 1.39728e-05 1.48341e-05 1.42499e-05 1.39691e-05 1.60443e-05 1.84207e-05 1.92341e-05 1.86549e-05 1.90099e-05 2.06351e-05 2.15964e-05 2.08065e-05 1.77105e-05 1.41432e-05 1.35144e-05 1.56896e-05 1.68285e-05 1.5951e-05 1.61085e-05 1.64512e-05 1.41941e-05 1.23741e-05 1.43468e-05 1.75948e-05 1.85474e-05 1.69891e-05 1.45352e-05 1.26316e-05 1.2526e-05 1.36673e-05 1.36822e-05 1.29158e-05 1.29988e-05 1.23039e-05 9.72848e-06 7.88055e-06 8.37609e-06 9.5053e-06 9.56726e-06 9.14112e-06 1.01519e-05 1.23531e-05 1.39929e-05 1.59533e-05 1.83195e-05 1.77506e-05 1.37332e-05 1.02783e-05 9.57734e-06 9.6693e-06 8.81962e-06 7.90569e-06 8.47878e-06 1.05358e-05 1.14681e-05 9.87378e-06 8.814e-06 1.02518e-05 1.27537e-05 1.53422e-05 1.69009e-05 1.61298e-05 1.34306e-05 1.0441e-05 9.03097e-06 9.01432e-06 8.40638e-06 7.25635e-06 7.32944e-06 9.48217e-06 1.28615e-05 1.38254e-05 1.07839e-05 8.35457e-06 8.54109e-06 8.43077e-06 7.53777e-06 7.41696e-06 8.81236e-06 1.05766e-05 1.1259e-05 1.12798e-05 1.05643e-05 8.86332e-06 8.4673e-06 1.08127e-05 1.27172e-05 1.18525e-05 1.11283e-05 1.20591e-05 1.17808e-05 9.7386e-06 9.28237e-06 1.1478e-05 1.26866e-05 1.07381e-05 9.22196e-06 1.04898e-05 1.16261e-05 1.15423e-05 1.27891e-05 1.55301e-05 1.61045e-05 1.36233e-05 1.15996e-05 1.10605e-05 1.11021e-05 1.10261e-05 9.79222e-06 8.85501e-06 9.39054e-06 1.05067e-05 1.16379e-05 1.13557e-05 9.81548e-06 9.423e-06 9.55281e-06 8.47422e-06 7.89706e-06 9.35228e-06 1.0473e-05 1.0216e-05 1.15463e-05 1.43787e-05 1.55592e-05 1.44508e-05 1.12896e-05 6.94068e-06 3.95156e-06 3.3299e-06 4.15401e-06 5.48846e-06 7.21153e-06 9.34017e-06 1.06734e-05 1.07663e-05 1.01849e-05 9.11467e-06 8.84646e-06 9.87091e-06 1.00019e-05 8.50504e-06 7.29894e-06 6.693e-06 5.53552e-06 4.77735e-06 5.73282e-06 6.70633e-06 5.94686e-06 5.18747e-06 6.57201e-06 9.619e-06 1.25915e-05 1.42858e-05 1.41724e-05 1.19321e-05 9.1377e-06 8.97053e-06 1.08231e-05 1.09527e-05 8.77434e-06 7.89527e-06 1.06721e-05 1.2475e-05 9.33289e-06 5.8005e-06 4.78472e-06 4.37156e-06 5.14988e-06 6.83156e-06 6.94346e-06 6.28655e-06 6.61597e-06 7.4341e-06 8.49038e-06 9.13089e-06 7.86697e-06 6.24324e-06 6.07141e-06 5.88139e-06 5.60228e-06 6.41153e-06 7.42233e-06 8.1817e-06 8.6531e-06 8.50606e-06 8.20163e-06 7.2987e-06 5.8019e-06 4.88931e-06 4.86592e-06 5.63876e-06 5.60356e-06 3.98612e-06 3.56375e-06 4.60402e-06 4.35041e-06 3.67214e-06 4.68156e-06 5.85094e-06 5.68185e-06 5.12386e-06 4.6721e-06 4.25657e-06 4.53429e-06 5.22991e-06 5.08247e-06 4.23089e-06 3.77159e-06 4.38053e-06 5.7634e-06 6.79702e-06 7.83401e-06 1.00464e-05 1.17424e-05 1.03442e-05 6.95688e-06 4.40142e-06 3.6394e-06 4.36432e-06 5.68383e-06 6.14567e-06 4.8666e-06 2.57287e-06 1.00503e-06 1.66118e-06 4.50486e-06 6.77834e-06 6.7807e-06 6.20458e-06 5.38122e-06 3.92146e-06 3.13773e-06 2.94932e-06 2.49671e-06 0.000130424 0.000515058 0.000771031
|
| 2 |
+
|
RNA-seq/15-Colo320_S15_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 15-Colo320_S15_L001_R1_001.fastq.gz, 15-Colo320_S15_L001_R2_001.fastq.gz], [ 15-Colo320_S15_L002_R1_001.fastq.gz, 15-Colo320_S15_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 29773109,
|
| 6 |
+
"num_assigned_fragments": 29773109,
|
| 7 |
+
"num_frags_with_consistent_mappings": 23341678,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 6431431,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 23341678,
|
| 15 |
+
"SF": 2445151,
|
| 16 |
+
"SR": 3986280,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/15-Colo320_S15_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,56 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:45:22.952] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:45:23.026] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:45:23.029] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:45:30.823] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:45:30.823] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:48:13.871] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
|
| 12 |
+
[2020-11-04 12:48:13.874] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
|
| 13 |
+
[2020-11-04 12:48:13.900] [jointLog] [info] Thread saw mini-batch with a maximum of 4.42% zero probability fragments
|
| 14 |
+
[2020-11-04 12:48:13.905] [jointLog] [info] Thread saw mini-batch with a maximum of 4.30% zero probability fragments
|
| 15 |
+
[2020-11-04 12:48:13.908] [jointLog] [info] Thread saw mini-batch with a maximum of 4.50% zero probability fragments
|
| 16 |
+
[2020-11-04 12:48:13.912] [jointLog] [info] Thread saw mini-batch with a maximum of 4.38% zero probability fragments
|
| 17 |
+
[2020-11-04 12:48:13.923] [jointLog] [info] Thread saw mini-batch with a maximum of 4.50% zero probability fragments
|
| 18 |
+
[2020-11-04 12:48:13.936] [jointLog] [info] Thread saw mini-batch with a maximum of 4.36% zero probability fragments
|
| 19 |
+
[2020-11-04 12:48:13.964] [jointLog] [info] Thread saw mini-batch with a maximum of 4.56% zero probability fragments
|
| 20 |
+
[2020-11-04 12:48:13.971] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
|
| 21 |
+
[2020-11-04 12:48:13.971] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments
|
| 22 |
+
[2020-11-04 12:48:13.975] [jointLog] [info] Thread saw mini-batch with a maximum of 4.34% zero probability fragments
|
| 23 |
+
[2020-11-04 12:48:15.332] [fileLog] [info]
|
| 24 |
+
At end of round 0
|
| 25 |
+
==================
|
| 26 |
+
Observed 69619954 total fragments (69619954 in most recent round)
|
| 27 |
+
|
| 28 |
+
[2020-11-04 12:48:15.332] [jointLog] [info] Computed 1,488,961 rich equivalence classes for further processing
|
| 29 |
+
[2020-11-04 12:48:15.332] [jointLog] [info] Counted 29,773,109 total reads in the equivalence classes
|
| 30 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] Number of mappings discarded because of alignment score : 17,528,289
|
| 31 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,774,391
|
| 32 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 33 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 211,511
|
| 34 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] Mapping rate = 42.7652%
|
| 35 |
+
|
| 36 |
+
[2020-11-04 12:48:15.348] [jointLog] [info] finished quantifyLibrary()
|
| 37 |
+
[2020-11-04 12:48:15.350] [jointLog] [info] Starting optimizer
|
| 38 |
+
[2020-11-04 12:48:15.721] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:48:15.785] [jointLog] [info] iteration = 0 | max rel diff. = 5251.52
|
| 40 |
+
[2020-11-04 12:48:22.124] [jointLog] [info] iteration = 100 | max rel diff. = 12.5181
|
| 41 |
+
[2020-11-04 12:48:28.954] [jointLog] [info] iteration = 200 | max rel diff. = 8.12998
|
| 42 |
+
[2020-11-04 12:48:35.843] [jointLog] [info] iteration = 300 | max rel diff. = 2.14191
|
| 43 |
+
[2020-11-04 12:48:42.629] [jointLog] [info] iteration = 400 | max rel diff. = 5.43497
|
| 44 |
+
[2020-11-04 12:48:49.226] [jointLog] [info] iteration = 500 | max rel diff. = 2.6871
|
| 45 |
+
[2020-11-04 12:48:55.789] [jointLog] [info] iteration = 600 | max rel diff. = 0.0390864
|
| 46 |
+
[2020-11-04 12:49:02.440] [jointLog] [info] iteration = 700 | max rel diff. = 1.49226
|
| 47 |
+
[2020-11-04 12:49:08.917] [jointLog] [info] iteration = 800 | max rel diff. = 1.67571
|
| 48 |
+
[2020-11-04 12:49:15.573] [jointLog] [info] iteration = 900 | max rel diff. = 0.0642987
|
| 49 |
+
[2020-11-04 12:49:22.239] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.283463
|
| 50 |
+
[2020-11-04 12:49:28.872] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.312545
|
| 51 |
+
[2020-11-04 12:49:35.555] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.160993
|
| 52 |
+
[2020-11-04 12:49:42.163] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.892853
|
| 53 |
+
[2020-11-04 12:49:47.287] [jointLog] [info] iteration = 1,377 | max rel diff. = 0.00925329
|
| 54 |
+
[2020-11-04 12:49:47.304] [jointLog] [info] Finished optimizer
|
| 55 |
+
[2020-11-04 12:49:47.304] [jointLog] [info] writing output
|
| 56 |
+
|
RNA-seq/16-HCC44_S16_L001_R1_001.fastq.gz
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:07271d4c72485148d934aa75e00d41c883cbafc8d8e8eba1533828acd3db140c
|
| 3 |
+
size 464225631
|
RNA-seq/16-HCC44_S16_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/16-HCC44_S16_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 761059,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 29173177,
|
| 35 |
+
"num_mapped": 17801313,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 118182,
|
| 38 |
+
"num_fragments_filtered_vm": 500810,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 3240832,
|
| 40 |
+
"percent_mapped": 61.01945290360389,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:51:10 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:52:54 2020"
|
| 44 |
+
}
|
RNA-seq/16-HCC44_S16_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"16-HCC44_S16_L001_R1_001.fastq.gz",
|
| 8 |
+
"16-HCC44_S16_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"16-HCC44_S16_L001_R2_001.fastq.gz",
|
| 12 |
+
"16-HCC44_S16_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "16-HCC44_S16_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|
RNA-seq/16-HCC44_S16_salmon/libParams/flenDist.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1.73939e-43 2.59266e-43 3.85831e-43 5.73264e-43 8.50388e-43 1.25946e-42 1.86234e-42 2.74939e-42 4.05248e-42 5.96362e-42 8.76202e-42 1.2853e-41 1.88238e-41 2.75244e-41 4.01822e-41 5.85671e-41 8.52274e-41 1.23826e-40 1.79617e-40 2.60128e-40 3.76127e-40 5.42983e-40 7.82605e-40 1.12617e-39 1.61798e-39 2.32084e-39 3.32371e-39 4.75232e-39 6.78413e-39 9.66913e-39 1.3759e-38 1.95475e-38 2.77268e-38 3.92657e-38 5.55179e-38 7.83715e-38 1.10456e-37 1.55426e-37 2.18355e-37 3.43933e-14 2.42242e-08 9.68989e-08 1.68053e-07 2.49048e-07 4.74871e-07 7.78525e-07 8.73696e-07 1.13092e-06 2.98607e-06 6.33498e-06 9.10894e-06 2.17397e-05 6.3981e-05 0.000128348 0.000191814 0.000247607 0.0002782 0.000260748 0.000219399 0.00020217 0.000209507 0.000210976 0.000203578 0.000198285 0.000201046 0.000217471 0.000239043 0.000256002 0.000273743 0.000288749 0.000294875 0.000303306 0.000318845 0.000341982 0.000385528 0.000432037 0.000452128 0.000491802 0.000613507 0.000765281 0.000830187 0.00079604 0.000731473 0.000663554 0.000626272 0.000668924 0.000771233 0.000834168 0.000805537 0.000763798 0.000767592 0.000790987 0.000811392 0.000825482 0.000846738 0.000886661 0.000943155 0.00102089 0.00110906 0.001176 0.00121935 0.00126015 0.00128881 0.00130394 0.00135587 0.0014449 0.00150034 0.00152509 0.00158821 0.00169362 0.00178959 0.00186617 0.0019514 0.00201339 0.00202706 0.00207309 0.00217798 0.00227956 0.00237068 0.00246281 0.00256086 0.00268627 0.0028149 0.00291127 0.00300155 0.00311446 0.00323312 0.0033505 0.00347606 0.0036177 0.00380284 0.00399253 0.00410315 0.00417643 0.00427675 0.00437124 0.0044718 0.00460014 0.00466658 0.00465665 0.00467138 0.00471594 0.0047544 0.00479957 0.00485808 0.00495478 0.00507465 0.00512778 0.0051305 0.00518023 0.00525848 0.00540356 0.00569981 0.00587753 0.00570435 0.00545856 0.00539089 0.00545983 0.00559922 0.00574695 0.00585428 0.00592099 0.00595917 0.0060316 0.00621281 0.00641387 0.00647673 0.00642166 0.00636335 0.0063506 0.00640144 0.00648548 0.00648915 0.00650982 0.00682033 0.00724174 0.00755952 0.00804484 0.00859536 0.00869805 0.00821541 0.00740729 0.00665986 0.00617203 0.00590293 0.00578368 0.00576299 0.00582662 0.00597222 0.00632566 0.00701664 0.0075035 0.00713397 0.00633739 0.00585215 0.00569032 0.00561084 0.00558424 0.00564084 0.0057086 0.00571541 0.00567261 0.00557219 0.00544766 0.00540974 0.00554658 0.00585255 0.00602681 0.00577911 0.00535167 0.00509895 0.00504503 0.00505274 0.00500359 0.00488524 0.00476022 0.0047043 0.0047276 0.00470932 0.00459434 0.00450034 0.00447957 0.00448106 0.00449934 0.0045178 0.00448137 0.00438202 0.00427835 0.00423702 0.00425065 0.00423026 0.00413784 0.00404751 0.00399171 0.00394773 0.00394898 0.00399085 0.0039911 0.00392877 0.00384936 0.00377653 0.00370903 0.00363691 0.00355934 0.00349462 0.00345425 0.00342938 0.00341169 0.00340856 0.00340651 0.00335538 0.00324845 0.00315378 0.00310459 0.00307549 0.00305165 0.00303423 0.00304046 0.00305218 0.00301011 0.00292446 0.00285929 0.0028331 0.00281744 0.00279445 0.00276082 0.00269708 0.00261718 0.00257599 0.00257777 0.00258583 0.00257005 0.00253038 0.00251802 0.00251814 0.00245423 0.00237127 0.00234247 0.00232019 0.00227147 0.00225213 0.00227936 0.00230769 0.00232046 0.00233105 0.00233843 0.00230978 0.00222609 0.00214967 0.00213908 0.00213335 0.00206511 0.00197988 0.00192742 0.00190476 0.00190918 0.00192211 0.00190746 0.00185657 0.00179359 0.0017331 0.00167145 0.00163606 0.00165478 0.00168533 0.00169063 0.00168306 0.00165323 0.0016019 0.00157098 0.00157721 0.00158625 0.0015603 0.00151084 0.00146509 0.00143241 0.00142596 0.00143611 0.00143544 0.00142596 0.00140356 0.00136331 0.00134608 0.0013528 0.00132912 0.00127888 0.00123305 0.00119968 0.00119787 0.00121623 0.00121657 0.00120472 0.00120571 0.00121259 0.00120154 0.00117704 0.00116941 0.00117283 0.00114915 0.00110619 0.00108143 0.00106521 0.00102782 0.000982066 0.000959786 0.000965477 0.000979431 0.000981632 0.000965566 0.000943205 0.000931594 0.000932234 0.000932581 0.000921102 0.000906044 0.000900978 0.000898825 0.00088735 0.000861774 0.000836059 0.000831036 0.000827334 0.000800352 0.00077654 0.000778392 0.000789328 0.00079807 0.00080351 0.000799533 0.000780777 0.000749601 0.000721862 0.000706447 0.000696198 0.000691264 0.000688435 0.000680184 0.000681485 0.000699106 0.000710168 0.000703469 0.000689162 0.000677414 0.000662809 0.000629639 0.000599707 0.000603114 0.000614575 0.000613994 0.000613404 0.000609305 0.000597399 0.00058313 0.000569248 0.000561337 0.000552191 0.000535781 0.000532442 0.000536353 0.00052378 0.000518663 0.000537212 0.000544215 0.000520911 0.000490509 0.000479844 0.000490703 0.000497721 0.000483896 0.000462402 0.000452024 0.00045428 0.000458149 0.000455489 0.000445374 0.000439438 0.000448659 0.000455644 0.000441599 0.000421933 0.000415316 0.000410751 0.000391587 0.000364056 0.000348255 0.000353196 0.000366964 0.00037265 0.000362892 0.000344298 0.000336805 0.000349387 0.000365372 0.000367321 0.000356835 0.000340751 0.000323272 0.000316429 0.000324679 0.00033078 0.00032495 0.00032673 0.000344718 0.000351139 0.000339639 0.000332792 0.000326614 0.000310297 0.000296398 0.000295995 0.000304152 0.000304748 0.000290623 0.000274139 0.000267404 0.000276636 0.000293343 0.000295518 0.000284532 0.000275012 0.000263855 0.00024957 0.000243656 0.000248261 0.000251877 0.000254541 0.000264022 0.000266712 0.000249706 0.000228683 0.00022026 0.00022179 0.000220883 0.000213572 0.00021232 0.000217552 0.000214673 0.000211233 0.000219593 0.000227463 0.000226154 0.000220653 0.000212988 0.000206209 0.000204919 0.000204788 0.000200147 0.000195449 0.000189715 0.000181437 0.000183534 0.000194387 0.000196954 0.000190408 0.000182093 0.000176547 0.00017704 0.000178384 0.000177625 0.000182242 0.000191094 0.000191042 0.000180034 0.00016933 0.000161653 0.0001509 0.000141406 0.000144295 0.000153927 0.000153441 0.00014475 0.000139374 0.000136299 0.000138642 0.000149693 0.000153592 0.000140512 0.00012483 0.000121926 0.000127475 0.00012866 0.000126167 0.000127348 0.000130501 0.000129702 0.000125048 0.00012572 0.00013417 0.000137205 0.000129117 0.000119276 0.000112157 0.000105817 0.000103398 0.000106491 0.000111916 0.00011699 0.000117938 0.000114376 0.00011016 0.000110959 0.000118322 0.000121635 0.000115532 0.000107494 0.000102462 0.000102927 0.000108039 0.000111327 0.000110951 0.000108051 0.00010215 9.74058e-05 9.75837e-05 9.7651e-05 9.34998e-05 8.83822e-05 8.63839e-05 8.98046e-05 9.47281e-05 9.38864e-05 9.05448e-05 9.26976e-05 9.66306e-05 9.37962e-05 8.65265e-05 8.23267e-05 8.37307e-05 8.91774e-05 9.14385e-05 8.36297e-05 7.18437e-05 6.8952e-05 7.68191e-05 8.28207e-05 7.8413e-05 7.10314e-05 6.9502e-05 7.19731e-05 7.22682e-05 7.22805e-05 7.71489e-05 7.94583e-05 7.18758e-05 6.18509e-05 5.77524e-05 5.94445e-05 6.26921e-05 6.5623e-05 6.96847e-05 7.25606e-05 7.18218e-05 7.10223e-05 6.8763e-05 6.29182e-05 6.02114e-05 5.87582e-05 5.11327e-05 4.33958e-05 4.4218e-05 5.1865e-05 5.83047e-05 5.64172e-05 4.77585e-05 4.13965e-05 4.09663e-05 4.38296e-05 4.65923e-05 4.55363e-05 4.21323e-05 4.04152e-05 4.15198e-05 4.66758e-05 5.36648e-05 5.63863e-05 5.44393e-05 5.26114e-05 5.1095e-05 4.60745e-05 4.13754e-05 4.36568e-05 4.85804e-05 5.05572e-05 4.99574e-05 4.83777e-05 4.87665e-05 4.88668e-05 4.51224e-05 4.20471e-05 4.25445e-05 4.43969e-05 4.50293e-05 4.28589e-05 4.0137e-05 3.83102e-05 3.6136e-05 3.58915e-05 3.8274e-05 3.70673e-05 3.0284e-05 2.47751e-05 2.55939e-05 3.05122e-05 3.47651e-05 3.66747e-05 3.64324e-05 3.56231e-05 3.7812e-05 4.1351e-05 3.97316e-05 3.44346e-05 3.32764e-05 3.57218e-05 3.59683e-05 3.36295e-05 3.33151e-05 3.67262e-05 3.67361e-05 3.15156e-05 2.97582e-05 3.24718e-05 3.49514e-05 3.61764e-05 3.5234e-05 3.24872e-05 3.02919e-05 2.99705e-05 3.10881e-05 3.20915e-05 3.03581e-05 2.60993e-05 2.43944e-05 2.55086e-05 2.37261e-05 1.93073e-05 1.89782e-05 2.43456e-05 2.97298e-05 3.00979e-05 2.52107e-05 2.0366e-05 2.13718e-05 2.68633e-05 3.01207e-05 2.79978e-05 2.45523e-05 2.35457e-05 2.52769e-05 2.86723e-05 2.89164e-05 2.41099e-05 1.92446e-05 1.70259e-05 1.63669e-05 1.70357e-05 1.9566e-05 2.23931e-05 2.12537e-05 1.55693e-05 1.22128e-05 1.53519e-05 1.97308e-05 2.04455e-05 1.94782e-05 1.94724e-05 1.93306e-05 1.80142e-05 1.71026e-05 1.70833e-05 1.64545e-05 1.5422e-05 1.5253e-05 1.62388e-05 1.74578e-05 1.78416e-05 1.85237e-05 1.91415e-05 1.69041e-05 1.45917e-05 1.70005e-05 2.04721e-05 1.89832e-05 1.56457e-05 1.67069e-05 1.91585e-05 1.7434e-05 1.44918e-05 1.44265e-05 1.54013e-05 1.56052e-05 1.58093e-05 1.59631e-05 1.57937e-05 1.56993e-05 1.60398e-05 1.66494e-05 1.63502e-05 1.53924e-05 1.64806e-05 2.01127e-05 2.21229e-05 2.0255e-05 1.78378e-05 1.71826e-05 1.66967e-05 1.49034e-05 1.29475e-05 1.2579e-05 1.3579e-05 1.53542e-05 1.69858e-05 1.70906e-05 1.56189e-05 1.32464e-05 1.21119e-05 1.33818e-05 1.43349e-05 1.33057e-05 1.16748e-05 1.10134e-05 1.2407e-05 1.46776e-05 1.4223e-05 1.08992e-05 9.05823e-06 1.00467e-05 1.06056e-05 9.52723e-06 8.70961e-06 8.70078e-06 9.54622e-06 1.21583e-05 1.49083e-05 1.50835e-05 1.29405e-05 1.05602e-05 9.9146e-06 1.16013e-05 1.44214e-05 1.54939e-05 1.30313e-05 9.45708e-06 7.4064e-06 6.78675e-06 7.41795e-06 9.77611e-06 1.28316e-05 1.44265e-05 1.46603e-05 1.4948e-05 1.43016e-05 1.18014e-05 9.45344e-06 8.45642e-06 7.77779e-06 7.31338e-06 7.50082e-06 7.43904e-06 7.41942e-06 8.7152e-06 9.91691e-06 9.19624e-06 7.11446e-06 5.30868e-06 4.91604e-06 5.25339e-06 5.06787e-06 4.51045e-06 3.91145e-06 3.28474e-06 3.11247e-06 4.62543e-06 8.14925e-06 1.0146e-05 8.35023e-06 6.27705e-06 5.86054e-06 5.64301e-06 6.15105e-06 7.60059e-06 7.46946e-06 5.10409e-06 3.53015e-06 4.42124e-06 5.68804e-06 6.21393e-06 7.85233e-06 1.05224e-05 1.0787e-05 7.57219e-06 4.49357e-06 4.34455e-06 5.52523e-06 6.05739e-06 6.81102e-06 7.69992e-06 6.9781e-06 5.4506e-06 4.89352e-06 5.32558e-06 6.07884e-06 7.0542e-06 7.92406e-06 7.21571e-06 5.42531e-06 5.04884e-06 6.09203e-06 6.98231e-06 7.77372e-06 8.85266e-06 9.20696e-06 8.5053e-06 7.82112e-06 7.05944e-06 6.07381e-06 5.72963e-06 5.55213e-06 4.74271e-06 3.78303e-06 3.50065e-06 4.61813e-06 6.98681e-06 8.63841e-06 7.675e-06 4.92304e-06 2.83584e-06 3.16124e-06 5.59375e-06 7.3621e-06 6.62527e-06 4.83212e-06 3.79323e-06 3.96628e-06 4.31157e-06 3.39319e-06 2.52561e-06 3.27886e-06 4.23553e-06 5.02703e-06 6.49125e-06 6.54919e-06 4.09444e-06 2.351e-06 3.29665e-06 4.92587e-06 5.0785e-06 3.88464e-06 2.86087e-06 2.6428e-06 2.73038e-06 3.14737e-06 3.54302e-06 3.52784e-06 4.03605e-06 4.52782e-06 3.47123e-06 2.07846e-06 2.09489e-06 3.11838e-06 4.38298e-06 4.88475e-06 3.86695e-06 2.60227e-06 2.49523e-06 3.49122e-06 4.5224e-06 4.5724e-06 3.85776e-06 3.12438e-06 3.27735e-06 4.45138e-06 5.34395e-06 6.34684e-06 8.35106e-06 9.25133e-06 7.85963e-06 5.77679e-06 4.35345e-06 3.79943e-06 3.3126e-06 2.54714e-06 2.00686e-06 1.69613e-06 1.70081e-06 1.89612e-06 1.90822e-06 2.33922e-06 3.58913e-06 4.81544e-06 5.2225e-06 5.17922e-06 4.62678e-06 3.04595e-06 2.17964e-06 3.68773e-06 5.86641e-06 6.19564e-06 4.78798e-06 3.48781e-06 2.68355e-06 1.93135e-06 2.02783e-06 3.57066e-06 5.38248e-06 5.98103e-06 5.12856e-06 3.48453e-06 2.34616e-06 3.28843e-06 5.92194e-06 6.97621e-06 5.12128e-06 3.07185e-06 2.30018e-06 2.19151e-06 2.56434e-06 2.87198e-06 2.82384e-06 2.96737e-06 3.13782e-06 3.03473e-06 3.08567e-06 3.5309e-06 4.0949e-06 4.0544e-06 3.06296e-06 1.89132e-06 1.44583e-06 1.79218e-06 2.1151e-06 1.9384e-06 1.9721e-06 2.60478e-06 2.964e-06 2.66474e-06 2.4388e-06 2.54304e-06 2.87706e-06 3.46572e-06 3.82491e-06 3.32419e-06 2.10463e-06 1.05541e-06 5.79258e-07 4.27142e-07 5.04942e-07 6.97055e-07 9.79877e-07 1.67698e-06 2.44656e-06 2.26446e-06 1.2568e-06 7.28887e-07 1.17805e-06 1.77271e-06 2.06496e-06 2.64378e-06 3.8678e-06 8.00695e-05 0.000304785 0.000452783
|
| 2 |
+
|
RNA-seq/16-HCC44_S16_salmon/lib_format_counts.json
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"read_files": "[ [ 16-HCC44_S16_L001_R1_001.fastq.gz, 16-HCC44_S16_L001_R2_001.fastq.gz], [ 16-HCC44_S16_L002_R1_001.fastq.gz, 16-HCC44_S16_L002_R2_001.fastq.gz] ]",
|
| 3 |
+
"expected_format": "ISR",
|
| 4 |
+
"compatible_fragment_ratio": 1.0,
|
| 5 |
+
"num_compatible_fragments": 17801313,
|
| 6 |
+
"num_assigned_fragments": 17801313,
|
| 7 |
+
"num_frags_with_consistent_mappings": 15224659,
|
| 8 |
+
"num_frags_with_inconsistent_or_orphan_mappings": 2576654,
|
| 9 |
+
"MSF": 0,
|
| 10 |
+
"OSF": 0,
|
| 11 |
+
"ISF": 0,
|
| 12 |
+
"MSR": 0,
|
| 13 |
+
"OSR": 0,
|
| 14 |
+
"ISR": 15224659,
|
| 15 |
+
"SF": 924551,
|
| 16 |
+
"SR": 1652103,
|
| 17 |
+
"MU": 0,
|
| 18 |
+
"OU": 0,
|
| 19 |
+
"IU": 0,
|
| 20 |
+
"U": 0
|
| 21 |
+
}
|
RNA-seq/16-HCC44_S16_salmon/logs/salmon_quant.log
ADDED
|
@@ -0,0 +1,54 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
|
| 2 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
|
| 3 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
|
| 4 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
|
| 5 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] parsing read library format
|
| 6 |
+
[2020-11-04 12:51:10.603] [jointLog] [info] There is 1 library.
|
| 7 |
+
[2020-11-04 12:51:10.693] [jointLog] [info] Loading Quasi index
|
| 8 |
+
[2020-11-04 12:51:10.695] [jointLog] [info] Loading 32-bit quasi index
|
| 9 |
+
[2020-11-04 12:51:18.439] [jointLog] [info] done
|
| 10 |
+
[2020-11-04 12:51:18.439] [jointLog] [info] Index contained 228,754 targets
|
| 11 |
+
[2020-11-04 12:52:23.169] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
|
| 12 |
+
[2020-11-04 12:52:23.178] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
|
| 13 |
+
[2020-11-04 12:52:23.185] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
|
| 14 |
+
[2020-11-04 12:52:23.200] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
|
| 15 |
+
[2020-11-04 12:52:23.216] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
|
| 16 |
+
[2020-11-04 12:52:23.219] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
|
| 17 |
+
[2020-11-04 12:52:23.226] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
|
| 18 |
+
[2020-11-04 12:52:23.237] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
|
| 19 |
+
[2020-11-04 12:52:23.251] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
|
| 20 |
+
[2020-11-04 12:52:23.259] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
|
| 21 |
+
[2020-11-04 12:52:23.274] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
|
| 22 |
+
[2020-11-04 12:52:23.275] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
|
| 23 |
+
[2020-11-04 12:52:23.891] [fileLog] [info]
|
| 24 |
+
At end of round 0
|
| 25 |
+
==================
|
| 26 |
+
Observed 29173177 total fragments (29173177 in most recent round)
|
| 27 |
+
|
| 28 |
+
[2020-11-04 12:52:23.891] [jointLog] [info] Computed 761,059 rich equivalence classes for further processing
|
| 29 |
+
[2020-11-04 12:52:23.891] [jointLog] [info] Counted 17,801,313 total reads in the equivalence classes
|
| 30 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] Number of mappings discarded because of alignment score : 3,240,832
|
| 31 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 500,810
|
| 32 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
|
| 33 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 118,182
|
| 34 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] Mapping rate = 61.0195%
|
| 35 |
+
|
| 36 |
+
[2020-11-04 12:52:23.910] [jointLog] [info] finished quantifyLibrary()
|
| 37 |
+
[2020-11-04 12:52:23.913] [jointLog] [info] Starting optimizer
|
| 38 |
+
[2020-11-04 12:52:24.171] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
|
| 39 |
+
[2020-11-04 12:52:24.197] [jointLog] [info] iteration = 0 | max rel diff. = 4999.15
|
| 40 |
+
[2020-11-04 12:52:26.847] [jointLog] [info] iteration = 100 | max rel diff. = 11.1931
|
| 41 |
+
[2020-11-04 12:52:29.570] [jointLog] [info] iteration = 200 | max rel diff. = 14.4542
|
| 42 |
+
[2020-11-04 12:52:32.329] [jointLog] [info] iteration = 300 | max rel diff. = 3.24777
|
| 43 |
+
[2020-11-04 12:52:34.859] [jointLog] [info] iteration = 400 | max rel diff. = 2.56899
|
| 44 |
+
[2020-11-04 12:52:37.554] [jointLog] [info] iteration = 500 | max rel diff. = 6.04014
|
| 45 |
+
[2020-11-04 12:52:40.182] [jointLog] [info] iteration = 600 | max rel diff. = 0.376957
|
| 46 |
+
[2020-11-04 12:52:42.862] [jointLog] [info] iteration = 700 | max rel diff. = 0.190514
|
| 47 |
+
[2020-11-04 12:52:45.355] [jointLog] [info] iteration = 800 | max rel diff. = 0.0949489
|
| 48 |
+
[2020-11-04 12:52:47.931] [jointLog] [info] iteration = 900 | max rel diff. = 0.198818
|
| 49 |
+
[2020-11-04 12:52:50.486] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.122703
|
| 50 |
+
[2020-11-04 12:52:53.222] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0890821
|
| 51 |
+
[2020-11-04 12:52:54.159] [jointLog] [info] iteration = 1,136 | max rel diff. = 0.00562987
|
| 52 |
+
[2020-11-04 12:52:54.181] [jointLog] [info] Finished optimizer
|
| 53 |
+
[2020-11-04 12:52:54.181] [jointLog] [info] writing output
|
| 54 |
+
|
RNA-seq/17-HEK293T-3_S17_salmon/aux_info/ambig_info.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
RNA-seq/17-HEK293T-3_S17_salmon/aux_info/meta_info.json
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"samp_type": "none",
|
| 4 |
+
"opt_type": "vb",
|
| 5 |
+
"quant_errors": [],
|
| 6 |
+
"num_libraries": 1,
|
| 7 |
+
"library_types": [
|
| 8 |
+
"ISR"
|
| 9 |
+
],
|
| 10 |
+
"frag_dist_length": 1001,
|
| 11 |
+
"seq_bias_correct": false,
|
| 12 |
+
"gc_bias_correct": false,
|
| 13 |
+
"num_bias_bins": 4096,
|
| 14 |
+
"mapping_type": "mapping",
|
| 15 |
+
"num_valid_targets": 228754,
|
| 16 |
+
"num_decoy_targets": 0,
|
| 17 |
+
"num_eq_classes": 1160354,
|
| 18 |
+
"serialized_eq_classes": false,
|
| 19 |
+
"eq_class_properties": [
|
| 20 |
+
"range_factorized"
|
| 21 |
+
],
|
| 22 |
+
"length_classes": [
|
| 23 |
+
539,
|
| 24 |
+
723,
|
| 25 |
+
1214,
|
| 26 |
+
2392,
|
| 27 |
+
104301
|
| 28 |
+
],
|
| 29 |
+
"index_seq_hash": "a88dfd39d4111a3be9390c28572775449c52b57824f4c9112b5685d24aee4edd",
|
| 30 |
+
"index_name_hash": "22abc86b365c289a4c33d2e2d16975f7631a75723823f5fee000f4d9d79d8415",
|
| 31 |
+
"index_seq_hash512": "6e2df13a76443d061f6d821afa1b0f848dac0ffb032d6be1a23a7826b758dd4672a580a656a10a023690e7b1df889c68e92051f91bcf9d9d81a66fe4d454386e",
|
| 32 |
+
"index_name_hash512": "f9b740308e77d6fc1f6b95fba3a4a3e12b59c77190a2fbaba46b6fd343cec404fbddff630e538aa326a75c8d711ac5e7952bb9c94030ebbe6ac96b45ee86f078",
|
| 33 |
+
"num_bootstraps": 0,
|
| 34 |
+
"num_processed": 42760454,
|
| 35 |
+
"num_mapped": 21296839,
|
| 36 |
+
"num_decoy_fragments": 0,
|
| 37 |
+
"num_dovetail_fragments": 154976,
|
| 38 |
+
"num_fragments_filtered_vm": 1005796,
|
| 39 |
+
"num_alignments_below_threshold_for_mapped_fragments_vm": 9253141,
|
| 40 |
+
"percent_mapped": 49.80498803871446,
|
| 41 |
+
"call": "quant",
|
| 42 |
+
"start_time": "Wed Nov 4 12:52:56 2020",
|
| 43 |
+
"end_time": "Wed Nov 4 12:55:55 2020"
|
| 44 |
+
}
|
RNA-seq/17-HEK293T-3_S17_salmon/cmd_info.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"salmon_version": "0.14.1",
|
| 3 |
+
"validateMappings": [],
|
| 4 |
+
"index": "gencode.v35.transcripts.salmon.index",
|
| 5 |
+
"libType": "ISR",
|
| 6 |
+
"mates1": [
|
| 7 |
+
"17-HEK293T-3_S17_L001_R1_001.fastq.gz",
|
| 8 |
+
"17-HEK293T-3_S17_L002_R1_001.fastq.gz"
|
| 9 |
+
],
|
| 10 |
+
"mates2": [
|
| 11 |
+
"17-HEK293T-3_S17_L001_R2_001.fastq.gz",
|
| 12 |
+
"17-HEK293T-3_S17_L002_R2_001.fastq.gz"
|
| 13 |
+
],
|
| 14 |
+
"threads": "12",
|
| 15 |
+
"output": "17-HEK293T-3_S17_salmon",
|
| 16 |
+
"auxDir": "aux_info"
|
| 17 |
+
}
|