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  5. RNA-seq/1-HEK293T-1_S1_L002_R2_001.fastq.gz +3 -0
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  16. RNA-seq/15-Colo320_S15_L002_R1_001.fastq.gz +3 -0
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  27. RNA-seq/2-LS174T_S2_salmon/cmd_info.json +17 -0
  28. RNA-seq/2-LS174T_S2_salmon/lib_format_counts.json +21 -0
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  30. RNA-seq/20-MDA453_S20_L001_R2_001.fastq.gz +3 -0
  31. RNA-seq/21-PC3_S21_L001_R2_001.fastq.gz +3 -0
  32. RNA-seq/22-SW620u_S22_salmon/aux_info/ambig_info.tsv +0 -0
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  38. RNA-seq/23-C42Bu_S23_L001_R2_001.fastq.gz +3 -0
  39. RNA-seq/23-C42Bu_S23_L002_R1_001.fastq.gz +3 -0
  40. RNA-seq/23-C42Bu_S23_salmon/aux_info/ambig_info.tsv +0 -0
  41. RNA-seq/23-C42Bu_S23_salmon/aux_info/meta_info.json +44 -0
  42. RNA-seq/23-C42Bu_S23_salmon/libParams/flenDist.txt +2 -0
  43. RNA-seq/23-C42Bu_S23_salmon/logs/salmon_quant.log +52 -0
  44. RNA-seq/24-H1299_S24_L001_R2_001.fastq.gz +3 -0
  45. RNA-seq/24-H1299_S24_salmon/aux_info/ambig_info.tsv +0 -0
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  49. RNA-seq/25-HCT116_S25_L001_R2_001.fastq.gz +3 -0
  50. RNA-seq/25-HCT116_S25_L002_R2_001.fastq.gz +3 -0
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2
+
RNA-seq/13-A549_S13_salmon/logs/salmon_quant.log ADDED
@@ -0,0 +1,57 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [2020-11-04 12:43:22.138] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
2
+ [2020-11-04 12:43:22.138] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
3
+ [2020-11-04 12:43:22.138] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
4
+ [2020-11-04 12:43:22.138] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
5
+ [2020-11-04 12:43:22.138] [jointLog] [info] parsing read library format
6
+ [2020-11-04 12:43:22.138] [jointLog] [info] There is 1 library.
7
+ [2020-11-04 12:43:22.210] [jointLog] [info] Loading Quasi index
8
+ [2020-11-04 12:43:22.212] [jointLog] [info] Loading 32-bit quasi index
9
+ [2020-11-04 12:43:29.949] [jointLog] [info] done
10
+ [2020-11-04 12:43:29.949] [jointLog] [info] Index contained 228,754 targets
11
+ [2020-11-04 12:43:50.287] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
12
+ [2020-11-04 12:43:50.307] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
13
+ [2020-11-04 12:43:50.309] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
14
+ [2020-11-04 12:43:50.339] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
15
+ [2020-11-04 12:43:50.339] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
16
+ [2020-11-04 12:43:50.345] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
17
+ [2020-11-04 12:43:50.347] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
18
+ [2020-11-04 12:43:50.348] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
19
+ [2020-11-04 12:43:50.350] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
20
+ [2020-11-04 12:43:50.373] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
21
+ [2020-11-04 12:43:50.379] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
22
+ [2020-11-04 12:43:50.393] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
23
+ [2020-11-04 12:43:50.746] [jointLog] [info] Computed 424,541 rich equivalence classes for further processing
24
+ [2020-11-04 12:43:50.746] [jointLog] [info] Counted 4,843,750 total reads in the equivalence classes
25
+ [2020-11-04 12:43:50.764] [jointLog] [info] Number of mappings discarded because of alignment score : 1,335,548
26
+ [2020-11-04 12:43:50.764] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 187,755
27
+ [2020-11-04 12:43:50.764] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
28
+ [2020-11-04 12:43:50.764] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 26,709
29
+ [2020-11-04 12:43:50.788] [jointLog] [warning] Only 4843750 fragments were mapped, but the number of burn-in fragments was set to 5000000.
30
+ The effective lengths have been computed using the observed mappings.
31
+
32
+ [2020-11-04 12:43:50.788] [jointLog] [info] Mapping rate = 52.6416%
33
+
34
+ [2020-11-04 12:43:50.788] [jointLog] [info] finished quantifyLibrary()
35
+ [2020-11-04 12:43:50.790] [jointLog] [info] Starting optimizer
36
+ [2020-11-04 12:43:50.746] [fileLog] [info]
37
+ At end of round 0
38
+ ==================
39
+ Observed 9201367 total fragments (9201367 in most recent round)
40
+
41
+ [2020-11-04 12:43:50.982] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
42
+ [2020-11-04 12:43:50.998] [jointLog] [info] iteration = 0 | max rel diff. = 1907
43
+ [2020-11-04 12:43:52.416] [jointLog] [info] iteration = 100 | max rel diff. = 16.9447
44
+ [2020-11-04 12:43:54.022] [jointLog] [info] iteration = 200 | max rel diff. = 3.3377
45
+ [2020-11-04 12:43:55.590] [jointLog] [info] iteration = 300 | max rel diff. = 0.404884
46
+ [2020-11-04 12:43:57.157] [jointLog] [info] iteration = 400 | max rel diff. = 2.76471
47
+ [2020-11-04 12:43:58.728] [jointLog] [info] iteration = 500 | max rel diff. = 0.455539
48
+ [2020-11-04 12:44:00.339] [jointLog] [info] iteration = 600 | max rel diff. = 0.283445
49
+ [2020-11-04 12:44:01.897] [jointLog] [info] iteration = 700 | max rel diff. = 10.1766
50
+ [2020-11-04 12:44:03.474] [jointLog] [info] iteration = 800 | max rel diff. = 0.569999
51
+ [2020-11-04 12:44:05.039] [jointLog] [info] iteration = 900 | max rel diff. = 0.0212041
52
+ [2020-11-04 12:44:06.663] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0828895
53
+ [2020-11-04 12:44:08.216] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0359577
54
+ [2020-11-04 12:44:08.983] [jointLog] [info] iteration = 1,150 | max rel diff. = 0.00604911
55
+ [2020-11-04 12:44:08.999] [jointLog] [info] Finished optimizer
56
+ [2020-11-04 12:44:08.999] [jointLog] [info] writing output
57
+
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+
RNA-seq/22-SW620u_S22_salmon/lib_format_counts.json ADDED
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+ {
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+ "read_files": "[ [ 22-SW620u_S22_L001_R1_001.fastq.gz, 22-SW620u_S22_L001_R2_001.fastq.gz], [ 22-SW620u_S22_L002_R1_001.fastq.gz, 22-SW620u_S22_L002_R2_001.fastq.gz] ]",
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+ "expected_format": "ISR",
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+ "compatible_fragment_ratio": 1.0,
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+ "num_compatible_fragments": 23610158,
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+ "num_assigned_fragments": 23610158,
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+ "num_frags_with_consistent_mappings": 19088602,
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+ }
RNA-seq/22-SW620u_S22_salmon/logs/salmon_quant.log ADDED
@@ -0,0 +1,56 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [2020-11-04 13:11:36.791] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
2
+ [2020-11-04 13:11:36.791] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
3
+ [2020-11-04 13:11:36.791] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
4
+ [2020-11-04 13:11:36.791] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
5
+ [2020-11-04 13:11:36.791] [jointLog] [info] parsing read library format
6
+ [2020-11-04 13:11:36.791] [jointLog] [info] There is 1 library.
7
+ [2020-11-04 13:11:36.873] [jointLog] [info] Loading Quasi index
8
+ [2020-11-04 13:11:36.874] [jointLog] [info] Loading 32-bit quasi index
9
+ [2020-11-04 13:11:44.809] [jointLog] [info] done
10
+ [2020-11-04 13:11:44.809] [jointLog] [info] Index contained 228,754 targets
11
+ [2020-11-04 13:13:37.919] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
12
+ [2020-11-04 13:13:37.926] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
13
+ [2020-11-04 13:13:37.944] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
14
+ [2020-11-04 13:13:37.958] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
15
+ [2020-11-04 13:13:37.973] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
16
+ [2020-11-04 13:13:37.984] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
17
+ [2020-11-04 13:13:37.988] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
18
+ [2020-11-04 13:13:38.016] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
19
+ [2020-11-04 13:13:38.019] [jointLog] [info] Thread saw mini-batch with a maximum of 3.96% zero probability fragments
20
+ [2020-11-04 13:13:38.021] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
21
+ [2020-11-04 13:13:38.035] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
22
+ [2020-11-04 13:13:38.074] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
23
+ [2020-11-04 13:13:39.201] [fileLog] [info]
24
+ At end of round 0
25
+ ==================
26
+ Observed 48771457 total fragments (48771457 in most recent round)
27
+
28
+ [2020-11-04 13:13:39.201] [jointLog] [info] Computed 1,149,824 rich equivalence classes for further processing
29
+ [2020-11-04 13:13:39.201] [jointLog] [info] Counted 23,610,158 total reads in the equivalence classes
30
+ [2020-11-04 13:13:39.218] [jointLog] [info] Number of mappings discarded because of alignment score : 10,400,367
31
+ [2020-11-04 13:13:39.218] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,147,834
32
+ [2020-11-04 13:13:39.218] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
33
+ [2020-11-04 13:13:39.218] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 150,251
34
+ [2020-11-04 13:13:39.218] [jointLog] [info] Mapping rate = 48.4098%
35
+
36
+ [2020-11-04 13:13:39.218] [jointLog] [info] finished quantifyLibrary()
37
+ [2020-11-04 13:13:39.221] [jointLog] [info] Starting optimizer
38
+ [2020-11-04 13:13:39.553] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
39
+ [2020-11-04 13:13:39.600] [jointLog] [info] iteration = 0 | max rel diff. = 5406.76
40
+ [2020-11-04 13:13:44.626] [jointLog] [info] iteration = 100 | max rel diff. = 18.6036
41
+ [2020-11-04 13:13:49.919] [jointLog] [info] iteration = 200 | max rel diff. = 7.65698
42
+ [2020-11-04 13:13:55.052] [jointLog] [info] iteration = 300 | max rel diff. = 10.4947
43
+ [2020-11-04 13:14:00.054] [jointLog] [info] iteration = 400 | max rel diff. = 4.68657
44
+ [2020-11-04 13:14:05.022] [jointLog] [info] iteration = 500 | max rel diff. = 10.3584
45
+ [2020-11-04 13:14:09.942] [jointLog] [info] iteration = 600 | max rel diff. = 2.12893
46
+ [2020-11-04 13:14:14.852] [jointLog] [info] iteration = 700 | max rel diff. = 0.0669968
47
+ [2020-11-04 13:14:19.747] [jointLog] [info] iteration = 800 | max rel diff. = 0.723358
48
+ [2020-11-04 13:14:24.672] [jointLog] [info] iteration = 900 | max rel diff. = 0.0423873
49
+ [2020-11-04 13:14:29.659] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.524445
50
+ [2020-11-04 13:14:34.664] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.493892
51
+ [2020-11-04 13:14:39.581] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.525381
52
+ [2020-11-04 13:14:44.526] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0381671
53
+ [2020-11-04 13:14:46.254] [jointLog] [info] iteration = 1,336 | max rel diff. = 0.00349754
54
+ [2020-11-04 13:14:46.282] [jointLog] [info] Finished optimizer
55
+ [2020-11-04 13:14:46.282] [jointLog] [info] writing output
56
+
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+ "call": "quant",
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+ "start_time": "Wed Nov 4 13:16:09 2020",
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+ "end_time": "Wed Nov 4 13:18:00 2020"
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+ }
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2
+
RNA-seq/23-C42Bu_S23_salmon/logs/salmon_quant.log ADDED
@@ -0,0 +1,52 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [2020-11-04 13:16:09.835] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
2
+ [2020-11-04 13:16:09.835] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
3
+ [2020-11-04 13:16:09.835] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4
4
+ [2020-11-04 13:16:09.835] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2.
5
+ [2020-11-04 13:16:09.835] [jointLog] [info] parsing read library format
6
+ [2020-11-04 13:16:09.835] [jointLog] [info] There is 1 library.
7
+ [2020-11-04 13:16:09.924] [jointLog] [info] Loading Quasi index
8
+ [2020-11-04 13:16:09.927] [jointLog] [info] Loading 32-bit quasi index
9
+ [2020-11-04 13:16:17.882] [jointLog] [info] done
10
+ [2020-11-04 13:16:17.882] [jointLog] [info] Index contained 228,754 targets
11
+ [2020-11-04 13:17:24.184] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
12
+ [2020-11-04 13:17:24.186] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
13
+ [2020-11-04 13:17:24.188] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
14
+ [2020-11-04 13:17:24.192] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
15
+ [2020-11-04 13:17:24.193] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
16
+ [2020-11-04 13:17:24.199] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
17
+ [2020-11-04 13:17:24.216] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
18
+ [2020-11-04 13:17:24.254] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
19
+ [2020-11-04 13:17:24.260] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
20
+ [2020-11-04 13:17:24.273] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
21
+ [2020-11-04 13:17:24.285] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
22
+ [2020-11-04 13:17:24.296] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
23
+ [2020-11-04 13:17:24.995] [fileLog] [info]
24
+ At end of round 0
25
+ ==================
26
+ Observed 28798750 total fragments (28798750 in most recent round)
27
+
28
+ [2020-11-04 13:17:24.994] [jointLog] [info] Computed 872,521 rich equivalence classes for further processing
29
+ [2020-11-04 13:17:24.994] [jointLog] [info] Counted 14,293,771 total reads in the equivalence classes
30
+ [2020-11-04 13:17:25.011] [jointLog] [info] Number of mappings discarded because of alignment score : 5,256,785
31
+ [2020-11-04 13:17:25.011] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 631,356
32
+ [2020-11-04 13:17:25.011] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
33
+ [2020-11-04 13:17:25.011] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings : 97,624
34
+ [2020-11-04 13:17:25.011] [jointLog] [info] Mapping rate = 49.6333%
35
+
36
+ [2020-11-04 13:17:25.012] [jointLog] [info] finished quantifyLibrary()
37
+ [2020-11-04 13:17:25.014] [jointLog] [info] Starting optimizer
38
+ [2020-11-04 13:17:25.259] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
39
+ [2020-11-04 13:17:25.292] [jointLog] [info] iteration = 0 | max rel diff. = 4432.4
40
+ [2020-11-04 13:17:28.791] [jointLog] [info] iteration = 100 | max rel diff. = 15.5024
41
+ [2020-11-04 13:17:32.383] [jointLog] [info] iteration = 200 | max rel diff. = 11.7464
42
+ [2020-11-04 13:17:35.972] [jointLog] [info] iteration = 300 | max rel diff. = 0.401413
43
+ [2020-11-04 13:17:39.460] [jointLog] [info] iteration = 400 | max rel diff. = 5.13623
44
+ [2020-11-04 13:17:42.966] [jointLog] [info] iteration = 500 | max rel diff. = 1.31092
45
+ [2020-11-04 13:17:46.436] [jointLog] [info] iteration = 600 | max rel diff. = 0.0719929
46
+ [2020-11-04 13:17:49.912] [jointLog] [info] iteration = 700 | max rel diff. = 0.486246
47
+ [2020-11-04 13:17:53.495] [jointLog] [info] iteration = 800 | max rel diff. = 2.68983
48
+ [2020-11-04 13:17:57.116] [jointLog] [info] iteration = 900 | max rel diff. = 0.0798411
49
+ [2020-11-04 13:17:59.866] [jointLog] [info] iteration = 979 | max rel diff. = 0.0083685
50
+ [2020-11-04 13:17:59.893] [jointLog] [info] Finished optimizer
51
+ [2020-11-04 13:17:59.893] [jointLog] [info] writing output
52
+
RNA-seq/24-H1299_S24_L001_R2_001.fastq.gz ADDED
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1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:074218eded28c0c887523f47b13e6adba79addb439d017105e8ab3c5f312e7f1
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+ size 444283636
RNA-seq/24-H1299_S24_salmon/aux_info/ambig_info.tsv ADDED
The diff for this file is too large to render. See raw diff
 
RNA-seq/24-H1299_S24_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
+ "24-H1299_S24_L001_R1_001.fastq.gz",
8
+ "24-H1299_S24_L002_R1_001.fastq.gz"
9
+ ],
10
+ "mates2": [
11
+ "24-H1299_S24_L001_R2_001.fastq.gz",
12
+ "24-H1299_S24_L002_R2_001.fastq.gz"
13
+ ],
14
+ "threads": "12",
15
+ "output": "24-H1299_S24_salmon",
16
+ "auxDir": "aux_info"
17
+ }
RNA-seq/24-H1299_S24_salmon/libParams/flenDist.txt ADDED
@@ -0,0 +1,2 @@
 
 
 
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