diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb index 75e41e2f410c9a11e852942e4a350818de6b8a54..0ac866ad58a0bc8aaaeaa8c3984910dde79db73a 100644 --- a/ProcessFASTQ.ipynb +++ b/ProcessFASTQ.ipynb @@ -673,7 +673,7 @@ }, { "cell_type": "code", - "execution_count": 274, + "execution_count": 279, "metadata": { "collapsed": false }, @@ -682,7 +682,26 @@ "name": "stdout", "output_type": "stream", "text": [ - "28\tNM:i:0\n" + "@PG\tID:Bowtie\tVN:1.1.2\tCL:\"bowtie --wrapper basic-0 -S -v 3 -p 8 --time --best ref/2-Indexes/Yeast-Noncoding/Yeast-Noncoding 3-Filtered/testing.fastq 4-Bowtied/testing.sam\"\n", + "SN279:493:C84L3ACXX:4:2309:1272:2215\t4\t*\t0\t0\t*\t*\t0\t0\tNGAGGACCGAACCGACTTACGTT\t#1=DDFFFGGHHHIIJIJIJJFH\tXM:i:0\n", + "SN279:493:C84L3ACXX:4:2309:1275:2239\t4\t*\t0\t0\t*\t*\t0\t0\tTCAGGTTACCCGCGACAGGACGGAA\tCC@DFDEDHHDFHEEFIIIIGIE:@\tXM:i:0\n", + "SN279:493:C84L3ACXX:4:2309:2182:2231\t4\t*\t0\t0\t*\t*\t0\t0\tAAGATCCCTCGAAGATGACGAGGT\tCCCFFD>DDCDDFH@AFHIJIGE?\tXM:i:0\n", + "SN279:493:C84L3ACXX:4:2309:1652:2216\t0\tRDN25-1\t2545\t255\t24M\t*\t0\t0\tNCACGTTCTAGCATTCAAGGTCCC\t#1=BDDDDFFDBBGHGEEIEHIII\tXA:i:1\tMD:Z:0C23\tNM:i:1\n", + "SN279:493:C84L3ACXX:4:2309:2260:2244\t0\tRDN58-1\t131\t255\t28M\t*\t0\t0\tAGGGGGCATGCCTGTTTGAGCGTCATTT\tCCCFFFFFHHHHHIGIJJIJJJJJJIJJ\tXA:i:0\tMD:Z:28\tNM:i:0\n", + "\n", + "\n", + "\n", + "\n", + "@SN279:493:C84L3ACXX:4:2309:1272:2215 1:N:0:CAGATC\n", + "NGAGGACCGAACCGACTTACGTT\n", + "+\n", + "#1=DDFFFGGHHHIIJIJIJJFH\n", + "@SN279:493:C84L3ACXX:4:2309:1309:2236 1:N:0:CAGATC\n", + "CTTTCTTTACTTATTCAATGAAGCGGA\n", + "+\n", + "CCCFFDFFHHHHHJJJJJJJJJJJJJJ\n", + "@SN279:493:C84L3ACXX:4:2309:1275:2239 1:N:0:CAGATC\n", + "TCAGGTTACCCGCGACAGGACGGAA\n" ] } ], @@ -690,7 +709,14 @@ "%%bash \n", "source ./source\n", "\n", - "sed -n 415,420p 4-Bowtied/$FILENAME.sam | hean" + "sed -n 415,420p 4-Bowtied/$FILENAME.sam\n", + "\n", + "echo\n", + "echo\n", + "echo\n", + "echo\n", + "\n", + "head 3-Filtered/$FILENAME.fastq" ] }, {