Hi all,
I am still learning how BOWTIE does its jobs, and now I got something that I do not understand. Basically what I did was just BOWTIE with the default options (bowtie -p 8 -q --solexa1.3-quals --sam-nohead -S) with human genome reference. When checking the sam output, I saw something like below:
My question concerns about those matches with * in their names and 0 in their positions in the reference. Can anybody explain to me what are those? Why these matches not in the reference and BOWTIE still reports them? How do I get the sam result without those matches?
Thanks,
D.
I am still learning how BOWTIE does its jobs, and now I got something that I do not understand. Basically what I did was just BOWTIE with the default options (bowtie -p 8 -q --solexa1.3-quals --sam-nohead -S) with human genome reference. When checking the sam output, I saw something like below:
Code:
HWUSI-EAS751_0001:1:1:0:852#0/1 16 gi|224589800|ref|NC_000001.10| 155633307 255 35M * 0 0 TGAGACCAGCCTGACCAACAAGGTGAAACCCCGTN CCCCA;ACCCCCCCCCCCCCCCBCCBBBAAAABB# XA:i:1 MD:Z:34C0 NM:i:1 HWUSI-EAS751_0001:1:1:0:823#0/1 16 gi|224589817|ref|NC_000005.9| 55233504 255 35M * 0 0 TAATCTTATCAGCACAATATAATCTAACAATACCN CCCCBCACCCCCCCCCCCCCCCC@CCCCCCCCBB# XA:i:1 MD:Z:34T0 NM:i:1 HWUSI-EAS751_0001:1:1:0:385#0/1 0 gi|224589811|ref|NC_000002.11| 230683139 255 35M * 0 0 NCAGTAACTGACACATCTCAATAACTGCCTGAAGC #CCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCAC XA:i:1 MD:Z:0C34 NM:i:1 HWUSI-EAS751_0001:1:1:0:1865#0/1 16 gi|224589805|ref|NC_000014.8| 47407772 255 35M * 0 0 ATCTGACCCCAATTAGAACAGCTATTATGAAAAAN BAB?B;AAC@CACBCCCBCCCBCCCCCCCCCCCC# XA:i:1 MD:Z:34G0 NM:i:1 HWUSI-EAS751_0001:1:1:0:1878#0/1 16 gi|224589821|ref|NC_000009.11| 132898793 255 35M * 0 0 GCAGGGGAACAGGTACCTCCGAGGGTGAGAGTCGN @;@BBBBBBAABBBAAAAA?BBBBBBBBBBBB?B# XA:i:1 MD:Z:34T0 NM:i:1 HWUSI-EAS751_0001:1:1:0:1348#0/1 0 gi|224589811|ref|NC_000002.11| 39229151 255 35M * 0 0 NTCCTTTCACTTAAGAACATGTTATGGCCAGGCGC #CCCCCCCCCCCCCCCCCCCCCCCCBABCCCCCBB XA:i:1 MD:Z:0C34 NM:i:1 HWUSI-EAS751_0001:1:1:0:1507#0/1 16 gi|224589800|ref|NC_000001.10| 15747351 255 35M * 0 0 CCCAAGCTGGTCTGAAACTCCTGGGCTCAAGTGAN A=@BCCBCCCCCCCCCCCBAABCCCCCCCCCCCC# XA:i:1 MD:Z:34T0 NM:i:1 HWUSI-EAS751_0001:1:1:0:69#0/1 16 gi|224589818|ref|NC_000006.11| 74229138 255 35M * 0 0 GGTCTCAAATTTCCACAAGGAGATATCAATGGTGN CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC# XA:i:1 MD:Z:34A0 NM:i:1 HWUSI-EAS751_0001:1:1:0:200#0/1 16 gi|224589809|ref|NC_000018.9| 55285040 255 35M * 0 0 GGGAGGCTGAGGCAGAAGAATCTCTTGAATCCGGN CCCCCCCCCCCCCCCCCCCB?B;@CCCCCB@ACC# XA:i:1 MD:Z:34G0 NM:i:1 HWUSI-EAS751_0001:1:1:0:418#0/1 4 * 0 0 * * 0 0 NATCGGAAGAGCGGTTCAGCAGGAATGCCGAGATC #BCCCCCBABCCACCCCAABAACCC@-@@9=8@>> XM:i:0 HWUSI-EAS751_0001:1:1:0:978#0/1 4 * 0 0 * * 0 0 NCTCGCCGACGCCTCTCATCTCACACCTGTCCACG ################################### XM:i:0
Thanks,
D.
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