Unit2-module2-ChIPseq/ChIP-seq.practice4.5.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2. Filter blacklisted regions from the bam file, name output SRR3001750_srt_dupr.chr2.chr11_flb.bam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cd /Users/yolandatiao/Documents/0_Bioinformatics2017/2018_Bioinformatics/Applied-Bioinformatics-HW-Yolanda/ChIP-seq.practice4.5\n",
    "bedtools intersect -abam SRR3001750_srt_dupr.chr2.chr11.bam -b mm10.blacklist.bed -v > SRR3001750_srt_dupr.chr2.chr11_flb.bam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 462024\n",
      "-rw-r--r--@ 1 yolandatiao  staff  102250566 Nov 12 15:30 SRR3001750_srt_dupr.chr2.chr11.bam\n",
      "-rw-r--r--  1 yolandatiao  staff  101887581 Nov 12 16:41 SRR3001750_srt_dupr.chr2.chr11_flb.bam\n",
      "-rw-r--r--@ 1 yolandatiao  staff       3767 Nov 12 13:19 mm10.blacklist.bed\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd /Users/yolandatiao/Documents/0_Bioinformatics2017/2018_Bioinformatics/Applied-Bioinformatics-HW-Yolanda/ChIP-seq.practice4.5\n",
    "ls -l"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 3. Filter out chr11 reads from SRR3001750_srt_dupr.chr2.chr11_flb.bam, name SRR3001750_srt_dupr.chr2.chr11_flb_flt.bam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 570568\n",
      "-rw-r--r--@ 1 yolandatiao  staff  102250566 Nov 12 15:30 SRR3001750_srt_dupr.chr2.chr11.bam\n",
      "-rw-r--r--  1 yolandatiao  staff  101887581 Nov 12 16:41 SRR3001750_srt_dupr.chr2.chr11_flb.bam\n",
      "-rw-r--r--  1 yolandatiao  staff   54968726 Nov 12 16:44 SRR3001750_srt_dupr.chr2.chr11_flb_flt.bam\n",
      "-rw-r--r--@ 1 yolandatiao  staff       3767 Nov 12 13:19 mm10.blacklist.bed\n",
      "SRR3001750.10646571\t16\tchr2\t3050671\t0\t28M1D22M\t*\t0\t0\tTAATGCCAGCACTCTGGAGGCAGTGGTAATGCAGAAGCAAGCAGGTTTCT\tJJJJJJJJIIHFHHJJJJJJJJJJIJJJJJJJJJJJJHHHHHFFFFFCCC\tAS:i:-19\tXS:i:-25\tXN:i:0\tXM:i:2\tXO:i:1\tXG:i:1\tNM:i:3\tMD:Z:28^G1G9G10\tYT:Z:UU\n",
      "SRR3001750.9755936\t0\tchr2\t3050860\t1\t50M\t*\t0\t0\tATAAAGAAAGAAAGAAACAAAGAAACAAAGAAACAAAGAAACAAAGAAAC\t+1?DBDEFHHHHHJJIJJIIJJJJJJJJJJJIGGGIIJIJIJIIJJJJII\tAS:i:-3\tXS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:1G48\tYT:Z:UU\n",
      "SRR3001750.1340458\t16\tchr2\t3051201\t42\t50M\t*\t0\t0\tGAGTTCGAGGCTTTTTCCCTAAAAAGTACTAGGGCTGAACCTGCGTGGTT\tEGCGGIIIIIIIIIIIGCIIIIEIIHCGIIIIIIHIIHHHGHFFDDD=8<\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n",
      "SRR3001750.403476\t0\tchr2\t3052163\t1\t50M\t*\t0\t0\tGGAGTGAGACAGTGGAGTTGTGGCAGTTCTGTTTGAGGTGGTCTGGGAAC\t@@CFDFFFHGHHHGGIJIGIIJEHHIIIJICEGH??BA9D=@*??DH?BB\tAS:i:0\tXS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n",
      "SRR3001750.3521352\t16\tchr2\t3052252\t30\t50M\t*\t0\t0\tGGAATTGAATCCCTGTCTTCTGAAAGGGTGGCTAGTATTCTTCACACCTG\tJJGIJIIHGEGIGIIHGGGCIJIIJJIGIIIJIJJJJHHHHHFDDDF@C@\tAS:i:0\tXS:i:-6\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n",
      "SRR3001750.8327062\t0\tchr2\t3052785\t42\t50M\t*\t0\t0\tCCGGCATGCTGGTGAAATTCAAAATGGGCAGCACAGCGAAGGGCAGCAGT\t=1:BDFFDHFBF<?FHIIJIJJJJIGCFGHJJIJJJJIJGH@GGIBHIGC\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:1T48\tYT:Z:UU\n",
      "SRR3001750.8465746\t16\tchr2\t3052787\t42\t48M\t*\t0\t0\tGGCATGCTGGTGAAATTCAAAATGGGCAGCACAGCGAAGGGCAGCAGT\tIJJJJJIIJJGHJJIHIIJJIHIJJJJIJIJIJIGFHHHHFFFFFC@@\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:48\tYT:Z:UU\n",
      "SRR3001750.7074175\t0\tchr2\t3052793\t42\t50M\t*\t0\t0\tCTGGTGAAATTCAAAATGGGCAGCACAGCGAAGGGCAGCAGTAGACTCTG\t@@@FDE4BFHDFFBEGHICGGGEEIJGHG1CFHGBGIIHGIHGDCHHEIC\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n",
      "SRR3001750.8023218\t16\tchr2\t3052897\t30\t50M\t*\t0\t0\tTACACCTAGATTGTAGACATGTCCCACAACACCTAGAGTATAGACATTTC\tFBF@IHGEGF?GFFFACGHGAE6;BEDGFFCGGGEIGFGHFFDB?BF@@@\tAS:i:0\tXS:i:-5\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n",
      "SRR3001750.12426695\t16\tchr2\t3052952\t42\t47M\t*\t0\t0\tGCATGAAGTCTATAGACCTGTCCCACTACACGAAGTCTATAGACATG\tF<HHAGIJIGGIIHFDDDJIGGHGHEGJIGJIJIFFFHBDADDB=+?\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:47\tYT:Z:UU\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "rm: SRR3001750_srt_dupr.chr2.chr11_flb_flt.sam: No such file or directory\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd /Users/yolandatiao/Documents/0_Bioinformatics2017/2018_Bioinformatics/Applied-Bioinformatics-HW-Yolanda/ChIP-seq.practice4.5\n",
    "#samtools view -h SRR3001750_srt_dupr.chr2.chr11_flb.bam | awk '{if ($3!=\"chr11\") {print $0}}' > SRR3001750_srt_dupr.chr2.chr11_flb_flt.sam\n",
    "#samtools view -bS SRR3001750_srt_dupr.chr2.chr11_flb_flt.sam > SRR3001750_srt_dupr.chr2.chr11_flb_flt.bam\n",
    "rm SRR3001750_srt_dupr.chr2.chr11_flb_flt.sam\n",
    "ls -l\n",
    "samtools view SRR3001750_srt_dupr.chr2.chr11_flb_flt.bam | head\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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