What is GSNAP's output format?

Question

[Joshua]

Hi,

This is my first time using GSNAP alignment tool, could anyone please let me know the output format? I've aligned paired fastq file to human mitochondrial genome, and I'm getting the output in the following format when I use the command cat SRR6423582.sam | grep "\bpaired\b".

>GACATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGTCTGTAATATTGAACGTAGGTGCGATAAATAATGGAATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGC    1 paired    B@@ABBCBBBAD@AABAABAABD@C@BABBBCCBBAABCBACCABBCCCCCCBBBDABCDABCEABD@ADCEABCCBCBECCC@ABDBAED@CCBCCCBCCEBCCCECDBDCDBCCCDCCCDCCCDCCBCCED@CCCCBDBBAEDBB>>@C SRR6423582.26694146
<CCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATC    1 paired    A=;AAABBBABCBBBBCBB?BBDABBDCCCDBADCBCDCCAACBCBBCCACCCDCC@BBCDDCDCDACCEDCCBBCBABCBBBD@ADCEBBBBBAEAEDCC@D@CCBEDBCBED@CDCCAEDFCDEBBACCEEDCBBDADFBDADBB?@BC SRR6423582.26694146
>AAAGCGGCTGTGCAGACATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGAATGAGGCAGGAATCAAAGACAGATACTGCGAC 1 paired    @@@CC@ACBD@DCBCBBBBACBBBAD@AABAABAABD@DABBCB/DDCCBBCCBBCCBBCCCCCCCBBBDABCDABCEABD@DACEABCCBCBECCC@ABDBAED@CCBCCCBCCEBCCCECDBDCDBCCCDCCCDCCCDCCBCCDB=AA  SRR6423582.26694148
<AAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGC 1 paired    A@?@:DC@@BBBB?@AC@@@BAAB@BBCDBCCACCB@CCEBACC.B>DBADC@ACCCAACBBABCCABCCDCC@B@AEBCDCDA/BEDCCABEBABCCBCD@ADC?BB1BBAEAEDCC@EA0D-BEC=CEDACEDDAEDF.<ACB@@3CC  SRR6423582.26694148
>ACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCC    1 paired    B?=@BEABBCBBBCA@CBABCBB@@BABAABB@BBBCBC@ABCCDCDCDACCEDCCBBEB@BCBBBD@ADCEBBBBBAEAEDCC@D@CCBDDCCBED@CDCC@DCEBBEDA@BCDDCCAACBCEAD@DCDABCDDEADDCBECCBC?@CB@ SRR6423582.26694171
<GGGTTTGGCAGAGATGTGTTTAAGTGCTGTGGCCAGAAGCGGGGGGAGGGGGGGGTTTGGTGGAAATTTTTTGTTATGATGTCTGTGTGGAAAGCGGCTGTGCAGACATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAA 1 paired    AA???ADACBCBCBBD@D@AAABC@DDCEAEBDACDCBDC@BBBBBBDBBBBBBB@=BDB@EBCCBBBBBBBE@B@BEBCEA:BDAE@EB@CAED@<A3DAEACDCC.1;:CC1CD=B@CC@C>7AE>.>B4<@@DDD>1?0/=A@A>@A  SRR6423582.26694171
>AAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTG 1 paired    B@BABCBCBB?BBDABBCBBBCA@CBABCBB@@BABAACC@CCBDBC@BBCDDCDCDACCEDCCBBEBABCBBBD@ADCEBBBBBAEAEDCC@D@CCBDDCCBED@BDCC@DCEBCDDA@BCDDCCAACBCEAD@DCDABCDCEACA?@C  SRR6423582.26694207

I'm not sure if I've done something wrong while aligning or this is the actual output format of GSNAP. If this is the default output format of GSNAP, could anyone please suggest me any tool to convert this output to SAM format?

Answer 1

[iraun]

Hi! In order to get a sam file you have to specify sam as output format using -A sam or --format=sam

[Joshua]

Thank you so much iraun I'm able to get correct result now. :)