Hi all,
there are some reads aligned. the .sam output file produced using bowtie, is like bellow and i want to extract aligned reads and their mapped positions on reference cromosome. I have read similar threads and found a sra format description but there are some differences! i need the position in reference sequence where each read has mapped.
@HD VN:1.0 SO:unsorted
@SQ SN:gi|224384765|gb|CM000666.1| LN:191154276
@PG ID:Bowtie VN:0.12.8 CL:"bowtie -q -n 3 -e 100 -l 50 -y -S -p 8 D:\a\index\ch4indexed D:\a\SRR017963.fastq D:\a\output_file.sam"
SRR017963.1 HWI-EAS153_5_30KE6AAXX:2:1:105:2042 length=76 4 * 0 0 * * 0 0 GTNNNTTNTTCTTGTGNTTTGAATTTAACCATGGAAGACAGTGATGGTGTAACTTATGCATTAAAGTGTGACAGTA :6!!!::!::::::::!:::::::::::::7777711131311331131111/13111101013/0/0111111/0 XM:i:0
SRR017963.3 HWI-EAS153_5_30KE6AAXX:2:1:194:1662 length=76 4 * 0 0 * * 0 0 GAATGCAATCATCATCGCACAGAATCGAATGGAATCATCGAATGGACTCGAATGGAATAATCATTGAACGGAATCG :7:21::60:71-1:--&:0:4440(3::310372&*/.2'-66/3+023/.,226-3323+2'02.,262323,2 XM:i:0
thanks for any advice.
there are some reads aligned. the .sam output file produced using bowtie, is like bellow and i want to extract aligned reads and their mapped positions on reference cromosome. I have read similar threads and found a sra format description but there are some differences! i need the position in reference sequence where each read has mapped.
@HD VN:1.0 SO:unsorted
@SQ SN:gi|224384765|gb|CM000666.1| LN:191154276
@PG ID:Bowtie VN:0.12.8 CL:"bowtie -q -n 3 -e 100 -l 50 -y -S -p 8 D:\a\index\ch4indexed D:\a\SRR017963.fastq D:\a\output_file.sam"
SRR017963.1 HWI-EAS153_5_30KE6AAXX:2:1:105:2042 length=76 4 * 0 0 * * 0 0 GTNNNTTNTTCTTGTGNTTTGAATTTAACCATGGAAGACAGTGATGGTGTAACTTATGCATTAAAGTGTGACAGTA :6!!!::!::::::::!:::::::::::::7777711131311331131111/13111101013/0/0111111/0 XM:i:0
SRR017963.3 HWI-EAS153_5_30KE6AAXX:2:1:194:1662 length=76 4 * 0 0 * * 0 0 GAATGCAATCATCATCGCACAGAATCGAATGGAATCATCGAATGGACTCGAATGGAATAATCATTGAACGGAATCG :7:21::60:71-1:--&:0:4440(3::310372&*/.2'-66/3+023/.,226-3323+2'02.,262323,2 XM:i:0
thanks for any advice.
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