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"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:05:33.604063Z",
"start_time": "2023-05-20T16:05:30.146945Z"
},
"collapsed": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2023-05-20 09:05:30-- https://www.mirbase.org/ftp/CURRENT/mature.fa.gz\r\n",
"Resolving www.mirbase.org... 130.88.97.249\r\n",
"Connecting to www.mirbase.org|130.88.97.249|:443... connected.\r\n",
"HTTP request sent, awaiting response... 200 OK\r\n",
"Length: 803746 (785K) [application/x-gzip]\r\n",
"Saving to: ‘mature.fa.gz’\r\n",
"\r\n",
"mature.fa.gz 100%[===================>] 784.91K 342KB/s in 2.3s \r\n",
"\r\n",
"2023-05-20 09:05:33 (342 KB/s) - ‘mature.fa.gz’ saved [803746/803746]\r\n",
"\r\n"
]
}
],
"source": [
"!wget https://www.mirbase.org/ftp/CURRENT/mature.fa.gz"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:08:16.201849Z",
"start_time": "2023-05-20T16:08:16.145057Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
">hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p\n",
"TGAGGTAGTAGGTTGTATAGTT\n",
">hsa-let-7a-3p MIMAT0004481 Homo sapiens let-7a-3p\n",
"CTATACAATCTACTGTCTTTC\n",
">hsa-let-7a-2-3p MIMAT0010195 Homo sapiens let-7a-2-3p\n",
"CTGTACAGCCTCCTAGCTTTCC\n",
">hsa-let-7b-5p MIMAT0000063 Homo sapiens let-7b-5p\n",
"TGAGGTAGTAGGTTGTGTGGTT\n",
">hsa-let-7b-3p MIMAT0004482 Homo sapiens let-7b-3p\n",
"CTATACAACCTACTGCCTTCCC\n"
]
}
],
"source": [
"%%bash\n",
"#extract human miRNAs\n",
"zcat mature.fa.gz | grep -A1 sapiens | sed '/^[^>]/s/U/T/g' > mature.hsa.fa\n",
"head mature.hsa.fa"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:14:51.607352Z",
"start_time": "2023-05-20T16:14:51.443975Z"
},
"collapsed": false
},
"outputs": [],
"source": [
"%%bash\n",
"samtools faidx mature.hsa.fa"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:10:22.921848Z",
"start_time": "2023-05-20T16:10:22.331328Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Settings:\n",
" Output files: \"mature_hsa.*.bt2\"\n",
" Line rate: 6 (line is 64 bytes)\n",
" Lines per side: 1 (side is 64 bytes)\n",
" Offset rate: 4 (one in 16)\n",
" FTable chars: 10\n",
" Strings: unpacked\n",
" Max bucket size: default\n",
" Max bucket size, sqrt multiplier: default\n",
" Max bucket size, len divisor: 4\n",
" Difference-cover sample period: 1024\n",
" Endianness: little\n",
" Actual local endianness: little\n",
" Sanity checking: disabled\n",
" Assertions: disabled\n",
" Random seed: 0\n",
" Sizeofs: void*:8, int:4, long:8, size_t:8\n",
"Input files DNA, FASTA:\n",
" mature.hsa.fa\n",
"Reading reference sizes\n",
" Time reading reference sizes: 00:00:00\n",
"Calculating joined length\n",
"Writing header\n",
"Reserving space for joined string\n",
"Joining reference sequences\n",
" Time to join reference sequences: 00:00:00\n",
"bmax according to bmaxDivN setting: 14346\n",
"Using parameters --bmax 10760 --dcv 1024\n",
" Doing ahead-of-time memory usage test\n",
" Passed! Constructing with these parameters: --bmax 10760 --dcv 1024\n",
"Constructing suffix-array element generator\n",
"Building DifferenceCoverSample\n",
" Building sPrime\n",
" Building sPrimeOrder\n",
" V-Sorting samples\n",
" V-Sorting samples time: 00:00:00\n",
" Allocating rank array\n",
" Ranking v-sort output\n",
" Ranking v-sort output time: 00:00:00\n",
" Invoking Larsson-Sadakane on ranks\n",
" Invoking Larsson-Sadakane on ranks time: 00:00:00\n",
" Sanity-checking and returning\n",
"Building samples\n",
"Reserving space for 12 sample suffixes\n",
"Generating random suffixes\n",
"QSorting 12 sample offsets, eliminating duplicates\n",
"QSorting sample offsets, eliminating duplicates time: 00:00:00\n",
"Multikey QSorting 12 samples\n",
" (Using difference cover)\n",
" Multikey QSorting samples time: 00:00:00\n",
"Calculating bucket sizes\n",
"Splitting and merging\n",
" Splitting and merging time: 00:00:00\n",
"Avg bucket size: 57386 (target: 10759)\n",
"Converting suffix-array elements to index image\n",
"Allocating ftab, absorbFtab\n",
"Entering Ebwt loop\n",
"Getting block 1 of 1\n",
" No samples; assembling all-inclusive block\n",
" Sorting block of length 57386 for bucket 1\n",
" (Using difference cover)\n",
" Sorting block time: 00:00:00\n",
"Returning block of 57387 for bucket 1\n",
"Exited Ebwt loop\n",
"fchr[A]: 0\n",
"fchr[C]: 12681\n",
"fchr[G]: 26180\n",
"fchr[T]: 42679\n",
"fchr[$]: 57386\n",
"Exiting Ebwt::buildToDisk()\n",
"Returning from initFromVector\n",
"Wrote 4393751 bytes to primary EBWT file: mature_hsa.1.bt2\n",
"Wrote 14352 bytes to secondary EBWT file: mature_hsa.2.bt2\n",
"Re-opening _in1 and _in2 as input streams\n",
"Returning from Ebwt constructor\n",
"Headers:\n",
" len: 57386\n",
" bwtLen: 57387\n",
" sz: 14347\n",
" bwtSz: 14347\n",
" lineRate: 6\n",
" offRate: 4\n",
" offMask: 0xfffffff0\n",
" ftabChars: 10\n",
" eftabLen: 20\n",
" eftabSz: 80\n",
" ftabLen: 1048577\n",
" ftabSz: 4194308\n",
" offsLen: 3587\n",
" offsSz: 14348\n",
" lineSz: 64\n",
" sideSz: 64\n",
" sideBwtSz: 48\n",
" sideBwtLen: 192\n",
" numSides: 299\n",
" numLines: 299\n",
" ebwtTotLen: 19136\n",
" ebwtTotSz: 19136\n",
" color: 0\n",
" reverse: 0\n",
"Total time for call to driver() for forward index: 00:00:00\n",
"Reading reference sizes\n",
" Time reading reference sizes: 00:00:00\n",
"Calculating joined length\n",
"Writing header\n",
"Reserving space for joined string\n",
"Joining reference sequences\n",
" Time to join reference sequences: 00:00:00\n",
" Time to reverse reference sequence: 00:00:00\n",
"bmax according to bmaxDivN setting: 14346\n",
"Using parameters --bmax 10760 --dcv 1024\n",
" Doing ahead-of-time memory usage test\n",
" Passed! Constructing with these parameters: --bmax 10760 --dcv 1024\n",
"Constructing suffix-array element generator\n",
"Building DifferenceCoverSample\n",
" Building sPrime\n",
" Building sPrimeOrder\n",
" V-Sorting samples\n",
" V-Sorting samples time: 00:00:00\n",
" Allocating rank array\n",
" Ranking v-sort output\n",
" Ranking v-sort output time: 00:00:00\n",
" Invoking Larsson-Sadakane on ranks\n",
" Invoking Larsson-Sadakane on ranks time: 00:00:00\n",
" Sanity-checking and returning\n",
"Building samples\n",
"Reserving space for 12 sample suffixes\n",
"Generating random suffixes\n",
"QSorting 12 sample offsets, eliminating duplicates\n",
"QSorting sample offsets, eliminating duplicates time: 00:00:00\n",
"Multikey QSorting 12 samples\n",
" (Using difference cover)\n",
" Multikey QSorting samples time: 00:00:00\n",
"Calculating bucket sizes\n",
"Splitting and merging\n",
" Splitting and merging time: 00:00:00\n",
"Avg bucket size: 57386 (target: 10759)\n",
"Converting suffix-array elements to index image\n",
"Allocating ftab, absorbFtab\n",
"Entering Ebwt loop\n",
"Getting block 1 of 1\n",
" No samples; assembling all-inclusive block\n",
" Sorting block of length 57386 for bucket 1\n",
" (Using difference cover)\n",
" Sorting block time: 00:00:00\n",
"Returning block of 57387 for bucket 1\n",
"Exited Ebwt loop\n",
"fchr[A]: 0\n",
"fchr[C]: 12681\n",
"fchr[G]: 26180\n",
"fchr[T]: 42679\n",
"fchr[$]: 57386\n",
"Exiting Ebwt::buildToDisk()\n",
"Returning from initFromVector\n",
"Wrote 4393751 bytes to primary EBWT file: mature_hsa.rev.1.bt2\n",
"Wrote 14352 bytes to secondary EBWT file: mature_hsa.rev.2.bt2\n",
"Re-opening _in1 and _in2 as input streams\n",
"Returning from Ebwt constructor\n",
"Headers:\n",
" len: 57386\n",
" bwtLen: 57387\n",
" sz: 14347\n",
" bwtSz: 14347\n",
" lineRate: 6\n",
" offRate: 4\n",
" offMask: 0xfffffff0\n",
" ftabChars: 10\n",
" eftabLen: 20\n",
" eftabSz: 80\n",
" ftabLen: 1048577\n",
" ftabSz: 4194308\n",
" offsLen: 3587\n",
" offsSz: 14348\n",
" lineSz: 64\n",
" sideSz: 64\n",
" sideBwtSz: 48\n",
" sideBwtLen: 192\n",
" numSides: 299\n",
" numLines: 299\n",
" ebwtTotLen: 19136\n",
" ebwtTotSz: 19136\n",
" color: 0\n",
" reverse: 1\n",
"Total time for backward call to driver() for mirror index: 00:00:00\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Building a SMALL index\n"
]
}
],
"source": [
"%%bash\n",
"#buile index\n",
"bowtie2-build mature.hsa.fa mature_hsa"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:30:35.241341Z",
"start_time": "2023-05-20T16:26:29.303820Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/A2508.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/A2508.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/A375.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/A375.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/A549.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/A549.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/BxPC3.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/BxPC3.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/C42Bu.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/C42Bu.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/Colo320.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/Colo320.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/H1299.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/H1299.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/H23u.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/H23u.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/H358u.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/H358u.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HCC44.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HCC44.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HCT116.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HCT116.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HEK293T-16.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HEK293T-16.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HEK293T-1.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HEK293T-1.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HEK293T-26.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HEK293T-26.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HEK293T-9.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HEK293T-9.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HEPG2.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HEPG2.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/HS707A.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/HS707A.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/K562.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/K562.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/LNCaP.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/LNCaP.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/LS174T.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/LS174T.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/MCF7.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/MCF7.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/MDA231.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/MDA231.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/MDA453.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/MDA453.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/PACA2.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/PACA2.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/PANC1.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/PANC1.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/PC3.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/PC3.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/SW480u.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/SW480u.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/SW620u.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/SW620u.hsa-miR.bam\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U fastq/ZR751.trim.fastq.gz | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/ZR751.hsa-miR.bam\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4821010 reads; of these:\n",
" 4821010 (100.00%) were unpaired; of these:\n",
" 4802725 (99.62%) aligned 0 times\n",
" 8705 (0.18%) aligned exactly 1 time\n",
" 9580 (0.20%) aligned >1 times\n",
"0.38% overall alignment rate\n",
"4776794 reads; of these:\n",
" 4776794 (100.00%) were unpaired; of these:\n",
" 4754325 (99.53%) aligned 0 times\n",
" 9945 (0.21%) aligned exactly 1 time\n",
" 12524 (0.26%) aligned >1 times\n",
"0.47% overall alignment rate\n",
"4955992 reads; of these:\n",
" 4955992 (100.00%) were unpaired; of these:\n",
" 4931131 (99.50%) aligned 0 times\n",
" 12243 (0.25%) aligned exactly 1 time\n",
" 12618 (0.25%) aligned >1 times\n",
"0.50% overall alignment rate\n",
"4932829 reads; of these:\n",
" 4932829 (100.00%) were unpaired; of these:\n",
" 4915807 (99.65%) aligned 0 times\n",
" 7826 (0.16%) aligned exactly 1 time\n",
" 9196 (0.19%) aligned >1 times\n",
"0.35% overall alignment rate\n",
"4553779 reads; of these:\n",
" 4553779 (100.00%) were unpaired; of these:\n",
" 4531848 (99.52%) aligned 0 times\n",
" 7366 (0.16%) aligned exactly 1 time\n",
" 14565 (0.32%) aligned >1 times\n",
"0.48% overall alignment rate\n",
"6464528 reads; of these:\n",
" 6464528 (100.00%) were unpaired; of these:\n",
" 6436582 (99.57%) aligned 0 times\n",
" 10498 (0.16%) aligned exactly 1 time\n",
" 17448 (0.27%) aligned >1 times\n",
"0.43% overall alignment rate\n",
"4489153 reads; of these:\n",
" 4489153 (100.00%) were unpaired; of these:\n",
" 4471925 (99.62%) aligned 0 times\n",
" 8902 (0.20%) aligned exactly 1 time\n",
" 8326 (0.19%) aligned >1 times\n",
"0.38% overall alignment rate\n",
"4019383 reads; of these:\n",
" 4019383 (100.00%) were unpaired; of these:\n",
" 3997543 (99.46%) aligned 0 times\n",
" 11181 (0.28%) aligned exactly 1 time\n",
" 10659 (0.27%) aligned >1 times\n",
"0.54% overall alignment rate\n",
"3655799 reads; of these:\n",
" 3655799 (100.00%) were unpaired; of these:\n",
" 3639679 (99.56%) aligned 0 times\n",
" 7308 (0.20%) aligned exactly 1 time\n",
" 8812 (0.24%) aligned >1 times\n",
"0.44% overall alignment rate\n",
"7007928 reads; of these:\n",
" 7007928 (100.00%) were unpaired; of these:\n",
" 6980739 (99.61%) aligned 0 times\n",
" 10843 (0.15%) aligned exactly 1 time\n",
" 16346 (0.23%) aligned >1 times\n",
"0.39% overall alignment rate\n",
"5966114 reads; of these:\n",
" 5966114 (100.00%) were unpaired; of these:\n",
" 5950253 (99.73%) aligned 0 times\n",
" 6855 (0.11%) aligned exactly 1 time\n",
" 9006 (0.15%) aligned >1 times\n",
"0.27% overall alignment rate\n",
"4217907 reads; of these:\n",
" 4217907 (100.00%) were unpaired; of these:\n",
" 4198913 (99.55%) aligned 0 times\n",
" 7085 (0.17%) aligned exactly 1 time\n",
" 11909 (0.28%) aligned >1 times\n",
"0.45% overall alignment rate\n",
"4101770 reads; of these:\n",
" 4101770 (100.00%) were unpaired; of these:\n",
" 4088791 (99.68%) aligned 0 times\n",
" 5288 (0.13%) aligned exactly 1 time\n",
" 7691 (0.19%) aligned >1 times\n",
"0.32% overall alignment rate\n",
"5970825 reads; of these:\n",
" 5970825 (100.00%) were unpaired; of these:\n",
" 5959974 (99.82%) aligned 0 times\n",
" 5437 (0.09%) aligned exactly 1 time\n",
" 5414 (0.09%) aligned >1 times\n",
"0.18% overall alignment rate\n",
"5948472 reads; of these:\n",
" 5948472 (100.00%) were unpaired; of these:\n",
" 5934365 (99.76%) aligned 0 times\n",
" 6041 (0.10%) aligned exactly 1 time\n",
" 8066 (0.14%) aligned >1 times\n",
"0.24% overall alignment rate\n",
"4079143 reads; of these:\n",
" 4079143 (100.00%) were unpaired; of these:\n",
" 4062616 (99.59%) aligned 0 times\n",
" 8477 (0.21%) aligned exactly 1 time\n",
" 8050 (0.20%) aligned >1 times\n",
"0.41% overall alignment rate\n",
"4486372 reads; of these:\n",
" 4486372 (100.00%) were unpaired; of these:\n",
" 4461801 (99.45%) aligned 0 times\n",
" 10688 (0.24%) aligned exactly 1 time\n",
" 13883 (0.31%) aligned >1 times\n",
"0.55% overall alignment rate\n",
"6052256 reads; of these:\n",
" 6052256 (100.00%) were unpaired; of these:\n",
" 6027059 (99.58%) aligned 0 times\n",
" 9673 (0.16%) aligned exactly 1 time\n",
" 15524 (0.26%) aligned >1 times\n",
"0.42% overall alignment rate\n",
"5058477 reads; of these:\n",
" 5058477 (100.00%) were unpaired; of these:\n",
" 5031761 (99.47%) aligned 0 times\n",
" 8373 (0.17%) aligned exactly 1 time\n",
" 18343 (0.36%) aligned >1 times\n",
"0.53% overall alignment rate\n",
"4495300 reads; of these:\n",
" 4495300 (100.00%) were unpaired; of these:\n",
" 4466388 (99.36%) aligned 0 times\n",
" 14500 (0.32%) aligned exactly 1 time\n",
" 14412 (0.32%) aligned >1 times\n",
"0.64% overall alignment rate\n",
"4878799 reads; of these:\n",
" 4878799 (100.00%) were unpaired; of these:\n",
" 4853373 (99.48%) aligned 0 times\n",
" 13422 (0.28%) aligned exactly 1 time\n",
" 12004 (0.25%) aligned >1 times\n",
"0.52% overall alignment rate\n",
"4911860 reads; of these:\n",
" 4911860 (100.00%) were unpaired; of these:\n",
" 4887113 (99.50%) aligned 0 times\n",
" 10158 (0.21%) aligned exactly 1 time\n",
" 14589 (0.30%) aligned >1 times\n",
"0.50% overall alignment rate\n",
"4908472 reads; of these:\n",
" 4908472 (100.00%) were unpaired; of these:\n",
" 4879950 (99.42%) aligned 0 times\n",
" 11657 (0.24%) aligned exactly 1 time\n",
" 16865 (0.34%) aligned >1 times\n",
"0.58% overall alignment rate\n",
"5741493 reads; of these:\n",
" 5741493 (100.00%) were unpaired; of these:\n",
" 5724200 (99.70%) aligned 0 times\n",
" 7739 (0.13%) aligned exactly 1 time\n",
" 9554 (0.17%) aligned >1 times\n",
"0.30% overall alignment rate\n",
"3805981 reads; of these:\n",
" 3805981 (100.00%) were unpaired; of these:\n",
" 3790834 (99.60%) aligned 0 times\n",
" 6854 (0.18%) aligned exactly 1 time\n",
" 8293 (0.22%) aligned >1 times\n",
"0.40% overall alignment rate\n",
"3026377 reads; of these:\n",
" 3026377 (100.00%) were unpaired; of these:\n",
" 3007927 (99.39%) aligned 0 times\n",
" 7559 (0.25%) aligned exactly 1 time\n",
" 10891 (0.36%) aligned >1 times\n",
"0.61% overall alignment rate\n",
"5734706 reads; of these:\n",
" 5734706 (100.00%) were unpaired; of these:\n",
" 5715120 (99.66%) aligned 0 times\n",
" 9143 (0.16%) aligned exactly 1 time\n",
" 10443 (0.18%) aligned >1 times\n",
"0.34% overall alignment rate\n",
"4477297 reads; of these:\n",
" 4477297 (100.00%) were unpaired; of these:\n",
" 4453612 (99.47%) aligned 0 times\n",
" 9742 (0.22%) aligned exactly 1 time\n",
" 13943 (0.31%) aligned >1 times\n",
"0.53% overall alignment rate\n",
"3595305 reads; of these:\n",
" 3595305 (100.00%) were unpaired; of these:\n",
" 3576052 (99.46%) aligned 0 times\n",
" 8967 (0.25%) aligned exactly 1 time\n",
" 10286 (0.29%) aligned >1 times\n",
"0.54% overall alignment rate\n"
]
}
],
"source": [
"%%bash\n",
"for f in fastq/*.trim.fastq.gz; do\n",
"out=${f/.trim.fastq.gz/.hsa-miR.bam}\n",
"out=`basename $out`\n",
"echo \"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U $f | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/$out\";\n",
"bowtie2 --sensitive --end-to-end -N 1 -p 12 -x mature_hsa -U $f | samtools view -q10 -F20 - -Sb -h -t mature.hsa.fa.fai -o bam/$out\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:31:34.910317Z",
"start_time": "2023-05-20T16:31:29.781463Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"samtools sort -o bam/A2508.hsa-miR.srt.bam bam/A2508.hsa-miR.bam\n",
"samtools sort -o bam/A375.hsa-miR.srt.bam bam/A375.hsa-miR.bam\n",
"samtools sort -o bam/A549.hsa-miR.srt.bam bam/A549.hsa-miR.bam\n",
"samtools sort -o bam/BxPC3.hsa-miR.srt.bam bam/BxPC3.hsa-miR.bam\n",
"samtools sort -o bam/C42Bu.hsa-miR.srt.bam bam/C42Bu.hsa-miR.bam\n",
"samtools sort -o bam/Colo320.hsa-miR.srt.bam bam/Colo320.hsa-miR.bam\n",
"samtools sort -o bam/H1299.hsa-miR.srt.bam bam/H1299.hsa-miR.bam\n",
"samtools sort -o bam/H23u.hsa-miR.srt.bam bam/H23u.hsa-miR.bam\n",
"samtools sort -o bam/H358u.hsa-miR.srt.bam bam/H358u.hsa-miR.bam\n",
"samtools sort -o bam/HCC44.hsa-miR.srt.bam bam/HCC44.hsa-miR.bam\n",
"samtools sort -o bam/HCT116.hsa-miR.srt.bam bam/HCT116.hsa-miR.bam\n",
"samtools sort -o bam/HEK293T-16.hsa-miR.srt.bam bam/HEK293T-16.hsa-miR.bam\n",
"samtools sort -o bam/HEK293T-1.hsa-miR.srt.bam bam/HEK293T-1.hsa-miR.bam\n",
"samtools sort -o bam/HEK293T-26.hsa-miR.srt.bam bam/HEK293T-26.hsa-miR.bam\n",
"samtools sort -o bam/HEK293T-9.hsa-miR.srt.bam bam/HEK293T-9.hsa-miR.bam\n",
"samtools sort -o bam/HEPG2.hsa-miR.srt.bam bam/HEPG2.hsa-miR.bam\n",
"samtools sort -o bam/HS707A.hsa-miR.srt.bam bam/HS707A.hsa-miR.bam\n",
"samtools sort -o bam/K562.hsa-miR.srt.bam bam/K562.hsa-miR.bam\n",
"samtools sort -o bam/LNCaP.hsa-miR.srt.bam bam/LNCaP.hsa-miR.bam\n",
"samtools sort -o bam/LS174T.hsa-miR.srt.bam bam/LS174T.hsa-miR.bam\n",
"samtools sort -o bam/MCF7.hsa-miR.srt.bam bam/MCF7.hsa-miR.bam\n",
"samtools sort -o bam/MDA231.hsa-miR.srt.bam bam/MDA231.hsa-miR.bam\n",
"samtools sort -o bam/MDA453.hsa-miR.srt.bam bam/MDA453.hsa-miR.bam\n",
"samtools sort -o bam/PACA2.hsa-miR.srt.bam bam/PACA2.hsa-miR.bam\n",
"samtools sort -o bam/PANC1.hsa-miR.srt.bam bam/PANC1.hsa-miR.bam\n",
"samtools sort -o bam/PC3.hsa-miR.srt.bam bam/PC3.hsa-miR.bam\n",
"samtools sort -o bam/SW480u.hsa-miR.srt.bam bam/SW480u.hsa-miR.bam\n",
"samtools sort -o bam/SW620u.hsa-miR.srt.bam bam/SW620u.hsa-miR.bam\n",
"samtools sort -o bam/ZR751.hsa-miR.srt.bam bam/ZR751.hsa-miR.bam\n"
]
}
],
"source": [
"%%bash\n",
"for f in bam/*.hsa-miR.bam; do\n",
"out=${f/.bam/.srt.bam};\n",
"echo \"samtools sort -o $out $f\";\n",
"samtools sort -m 2G -o $out $f\n",
"samtools index $out;\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:32:10.395458Z",
"start_time": "2023-05-20T16:32:10.342608Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"umi_tools dedup -I bam/A2508.hsa-miR.srt.bam -S bam/A2508.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/A375.hsa-miR.srt.bam -S bam/A375.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/A549.hsa-miR.srt.bam -S bam/A549.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/BxPC3.hsa-miR.srt.bam -S bam/BxPC3.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/C42Bu.hsa-miR.srt.bam -S bam/C42Bu.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/Colo320.hsa-miR.srt.bam -S bam/Colo320.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/H1299.hsa-miR.srt.bam -S bam/H1299.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/H23u.hsa-miR.srt.bam -S bam/H23u.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/H358u.hsa-miR.srt.bam -S bam/H358u.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HCC44.hsa-miR.srt.bam -S bam/HCC44.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HCT116.hsa-miR.srt.bam -S bam/HCT116.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HEK293T-16.hsa-miR.srt.bam -S bam/HEK293T-16.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HEK293T-1.hsa-miR.srt.bam -S bam/HEK293T-1.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HEK293T-26.hsa-miR.srt.bam -S bam/HEK293T-26.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HEK293T-9.hsa-miR.srt.bam -S bam/HEK293T-9.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HEPG2.hsa-miR.srt.bam -S bam/HEPG2.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/HS707A.hsa-miR.srt.bam -S bam/HS707A.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/K562.hsa-miR.srt.bam -S bam/K562.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/LNCaP.hsa-miR.srt.bam -S bam/LNCaP.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/LS174T.hsa-miR.srt.bam -S bam/LS174T.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/MCF7.hsa-miR.srt.bam -S bam/MCF7.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/MDA231.hsa-miR.srt.bam -S bam/MDA231.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/MDA453.hsa-miR.srt.bam -S bam/MDA453.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/PACA2.hsa-miR.srt.bam -S bam/PACA2.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/PANC1.hsa-miR.srt.bam -S bam/PANC1.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/PC3.hsa-miR.srt.bam -S bam/PC3.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/SW480u.hsa-miR.srt.bam -S bam/SW480u.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/SW620u.hsa-miR.srt.bam -S bam/SW620u.hsa-miR.srt.dd.bam &\n",
"umi_tools dedup -I bam/ZR751.hsa-miR.srt.bam -S bam/ZR751.hsa-miR.srt.dd.bam &\n"
]
}
],
"source": [
"%%bash\n",
"for f in bam/*.hsa-miR.srt.bam; do\n",
"out=${f/.srt.bam/.srt.dd.bam};\n",
"echo \"umi_tools dedup -I $f -S $out &\";\n",
"#umi_tools dedup -I $f -S $out &\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:33:55.460620Z",
"start_time": "2023-05-20T16:33:55.353828Z"
},
"collapsed": false
},
"outputs": [],
"source": [
"%%bash\n",
"for f in bam/*.hsa-miR.srt.dd.bam; do\n",
"samtools index $f &\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:39:03.632496Z",
"start_time": "2023-05-20T16:39:02.067991Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"bam/A2508.hsa-miR.srt.dd.bam\n",
"bam/A375.hsa-miR.srt.dd.bam\n",
"bam/A549.hsa-miR.srt.dd.bam\n",
"bam/BxPC3.hsa-miR.srt.dd.bam\n",
"bam/C42Bu.hsa-miR.srt.dd.bam\n",
"bam/Colo320.hsa-miR.srt.dd.bam\n",
"bam/H1299.hsa-miR.srt.dd.bam\n",
"bam/H23u.hsa-miR.srt.dd.bam\n",
"bam/H358u.hsa-miR.srt.dd.bam\n",
"bam/HCC44.hsa-miR.srt.dd.bam\n",
"bam/HCT116.hsa-miR.srt.dd.bam\n",
"bam/HEK293T-16.hsa-miR.srt.dd.bam\n",
"bam/HEK293T-1.hsa-miR.srt.dd.bam\n",
"bam/HEK293T-26.hsa-miR.srt.dd.bam\n",
"bam/HEK293T-9.hsa-miR.srt.dd.bam\n",
"bam/HEPG2.hsa-miR.srt.dd.bam\n",
"bam/HS707A.hsa-miR.srt.dd.bam\n",
"bam/K562.hsa-miR.srt.dd.bam\n",
"bam/LNCaP.hsa-miR.srt.dd.bam\n",
"bam/LS174T.hsa-miR.srt.dd.bam\n",
"bam/MCF7.hsa-miR.srt.dd.bam\n",
"bam/MDA231.hsa-miR.srt.dd.bam\n",
"bam/MDA453.hsa-miR.srt.dd.bam\n",
"bam/PACA2.hsa-miR.srt.dd.bam\n",
"bam/PANC1.hsa-miR.srt.dd.bam\n",
"bam/PC3.hsa-miR.srt.dd.bam\n",
"bam/SW480u.hsa-miR.srt.dd.bam\n",
"bam/SW620u.hsa-miR.srt.dd.bam\n",
"bam/ZR751.hsa-miR.srt.dd.bam\n"
]
}
],
"source": [
"%%bash\n",
"for f in bam/*.hsa-miR.srt.dd.bam; do\n",
"out=${f/.srt.dd.bam/.cnt};\n",
"out=`basename $out`\n",
"echo $f\n",
"samtools view $f | cut -f3 | sort | uniq -c | awk '{ print $2 \"\\t\" $1}' > count/$out\n",
"done"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:39:27.678503Z",
"start_time": "2023-05-20T16:39:24.308743Z"
},
"collapsed": false
},
"outputs": [],
"source": [
"import rpy2.ipython\n",
"%load_ext rpy2.ipython\n",
"import warnings\n",
"from rpy2.rinterface import RRuntimeWarning\n",
"warnings.filterwarnings(\"ignore\", category=RRuntimeWarning)"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:42:10.187793Z",
"start_time": "2023-05-20T16:42:09.845743Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" A2508 A375 A549 BxPC3 C42Bu Colo320 H1299 H23u H358u HCC44\n",
"hsa-let-7a-2-3p 1 9 1 0 0 0 0 0 0 0\n",
"hsa-let-7a-3p 30 65 29 32 66 36 13 10 13 31\n",
"hsa-let-7a-5p 838 843 929 894 1108 892 692 541 773 936\n",
"hsa-let-7b-3p 13 12 13 22 131 22 2 5 6 39\n",
"hsa-let-7b-5p 282 195 511 306 833 521 36 71 172 643\n",
"hsa-let-7c-5p 69 11 86 4 685 85 3 4 2 5\n",
" HCT116 HEK293T.1 HEK293T.16 HEK293T.26 HEK293T.9 HEPG2 HS707A\n",
"hsa-let-7a-2-3p 1 0 0 0 0 0 6\n",
"hsa-let-7a-3p 56 10 4 9 11 4 33\n",
"hsa-let-7a-5p 897 277 228 404 272 257 975\n",
"hsa-let-7b-3p 30 0 0 0 1 2 53\n",
"hsa-let-7b-5p 321 11 10 11 10 13 657\n",
"hsa-let-7c-5p 2 17 24 19 20 1 72\n",
" K562 LNCaP LS174T MCF7 MDA231 MDA453 PACA2 PANC1 PC3 SW480u\n",
"hsa-let-7a-2-3p 0 0 0 0 2 0 0 1 1 0\n",
"hsa-let-7a-3p 1 59 33 13 11 109 19 27 17 29\n",
"hsa-let-7a-5p 169 1113 753 755 1074 1205 768 838 983 789\n",
"hsa-let-7b-3p 1 47 64 4 10 65 16 23 9 27\n",
"hsa-let-7b-5p 9 822 435 211 261 906 221 361 475 498\n",
"hsa-let-7c-5p 2 966 4 91 3 34 5 6 0 2\n",
" SW620u ZR751\n",
"hsa-let-7a-2-3p 1 0\n",
"hsa-let-7a-3p 21 18\n",
"hsa-let-7a-5p 736 786\n",
"hsa-let-7b-3p 18 14\n",
"hsa-let-7b-5p 453 300\n",
"hsa-let-7c-5p 5 46\n"
]
}
],
"source": [
"%%R\n",
"files<-list.files(pattern=\".hsa-miR.cnt\", recursive=TRUE, full.names=TRUE)\n",
"datalist = lapply(files, function(x){read.table(file=x,header=FALSE,col.names=c(\"miRNA\", sub(\"./count/(\\\\S+).hsa-miR.cnt\", \"\\\\1\", x)))})\n",
"m <- Reduce(function(...) merge(..., by=1, all = TRUE), datalist)\n",
"rownames(m) <- m[,1]\n",
"m[is.na(m)] <- 0\n",
"m <- m[,-1]\n",
"head(m)"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:43:34.724737Z",
"start_time": "2023-05-20T16:43:22.580119Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"R[write to console]: Loading required package: S4Vectors\n",
"\n",
"R[write to console]: Loading required package: stats4\n",
"\n",
"R[write to console]: Loading required package: BiocGenerics\n",
"\n",
"R[write to console]: Loading required package: parallel\n",
"\n",
"R[write to console]: \n",
"Attaching package: ‘BiocGenerics’\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:parallel’:\n",
"\n",
" clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n",
" clusterExport, clusterMap, parApply, parCapply, parLapply,\n",
" parLapplyLB, parRapply, parSapply, parSapplyLB\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:stats’:\n",
"\n",
" IQR, mad, sd, var, xtabs\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:base’:\n",
"\n",
" anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n",
" dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n",
" grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n",
" order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n",
" rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n",
" union, unique, unsplit, which, which.max, which.min\n",
"\n",
"\n",
"R[write to console]: \n",
"Attaching package: ‘S4Vectors’\n",
"\n",
"\n",
"R[write to console]: The following object is masked from ‘package:base’:\n",
"\n",
" expand.grid\n",
"\n",
"\n",
"R[write to console]: Loading required package: IRanges\n",
"\n",
"R[write to console]: Loading required package: GenomicRanges\n",
"\n",
"R[write to console]: Loading required package: GenomeInfoDb\n",
"\n",
"R[write to console]: Loading required package: SummarizedExperiment\n",
"\n",
"R[write to console]: Loading required package: Biobase\n",
"\n",
"R[write to console]: Welcome to Bioconductor\n",
"\n",
" Vignettes contain introductory material; view with\n",
" 'browseVignettes()'. To cite Bioconductor, see\n",
" 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n",
"\n",
"\n",
"R[write to console]: Loading required package: DelayedArray\n",
"\n",
"R[write to console]: Loading required package: matrixStats\n",
"\n",
"R[write to console]: \n",
"Attaching package: ‘matrixStats’\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:Biobase’:\n",
"\n",
" anyMissing, rowMedians\n",
"\n",
"\n",
"R[write to console]: Loading required package: BiocParallel\n",
"\n",
"R[write to console]: \n",
"Attaching package: ‘DelayedArray’\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:matrixStats’:\n",
"\n",
" colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n",
"\n",
"\n",
"R[write to console]: The following objects are masked from ‘package:base’:\n",
"\n",
" aperm, apply, rowsum\n",
"\n",
"\n",
"R[write to console]: converting counts to integer mode\n",
"\n"
]
}
],
"source": [
"%%R\n",
"library(DESeq2)\n",
"colData <- data.frame(cond=colnames(m), row.names=colnames(m))\n",
"dds <- DESeqDataSetFromMatrix(countData = m, colData=colData, design = ~ cond)"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"ExecuteTime": {
"end_time": "2023-05-20T16:43:52.052339Z",
"start_time": "2023-05-20T16:43:51.814855Z"
},
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" A2508 A375 A549 BxPC3 C42Bu Colo320 H1299 \n",
" 1.0888061 1.2424944 1.0869263 1.0162428 1.0632169 1.6634946 1.0384271 \n",
" H23u H358u HCC44 HCT116 HEK293T.1 HEK293T.16 HEK293T.26 \n",
" 1.2745386 0.9586256 1.4011483 0.7453279 0.8418885 1.0259433 0.7463888 \n",
" HEK293T.9 HEPG2 HS707A K562 LNCaP LS174T MCF7 \n",
" 0.8957911 1.1909768 0.9530245 0.9804775 0.8729802 1.6712495 1.5413835 \n",
" MDA231 MDA453 PACA2 PANC1 PC3 SW480u SW620u \n",
" 1.0963836 1.4634479 1.0580141 1.0480069 0.8270327 1.0059966 1.1430368 \n",
" ZR751 \n",
" 1.0876778 \n"
]
}
],
"source": [
"%%R\n",
"dds <- estimateSizeFactors(dds)\n",
"sf <- sizeFactors(dds)\n",
"ncu <- counts(dds, normalized=TRUE)\n",
"write.table(m, file=\"miRNA_counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )\n",
"write.table(ncu, file=\"miRNA_norm-counts.txt\", sep=\"\\t\", quote=FALSE, col.names=NA )\n",
"sf"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 0
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