I am trying to work with the gmap/gsnap tools. I have fastq files and wanted to ask whether it make sense at all to try and convert the reads into fastA format so that I can work with the gmap tool.
I think, gmap work only with fastA but not with fastq, while gsnap can work with both.
I converted the fastq to fastA which looks like that:
>HWI-ST863:138:D0WT7ACXX:5:1101:1179:1941 1:N:0:GCCAAT ACTTACAGCATCCTCTCATCTGGGTTAACTTACTCTTGGAGGAGATGAAGGTCACTGTGCCTGGCTATCAAACCTTCCATGCTGCTCCACAGAGACAAAGA >HWI-ST863:138:D0WT7ACXX:5:1101:1577:1894 1:N:0:GCCAAT NTGTGAGTATGTGTGTTGTGAGAGAGAGTATGTTTGTGTGTGTGAATGTGTGTGTCTCTGTGAGTGTGTGTGTGTGAGAGTATGTTTGTGTGTGTGTGAAT >HWI-ST863:138:D0WT7ACXX:5:1101:1718:1912 1:N:0:GCCAAT CTGCCTCTTCACATCTCAAAAGGTGATTAACATCCGGAGATTTACATCATCTGCCAAGTCCTGCTGATCAAACAGCAGGGTAAGTATGGAGAAGGGCCACA ...
I created the indexed files with my fastA DNA file. It worked good, but when I am running the gmap, it gives me always the error message "no paths found"
and the files resulted is .nomapping .fa, which looks like that:
>HWI-ST863:138:D0WT7ACXX:5:1101:1403:1981 1:N:0:AGTCAA Paths (0): >HWI-ST863:138:D0WT7ACXX:5:1101:1470:1997 1:N:0:AGTCAA Paths (0): >HWI-ST863:138:D0WT7ACXX:5:1101:1677:1894 1:N:0:AGTCAA Paths (0): ...
Is there an explanation for this behavior? Is it possible to use this fastq-converted fastA files to run gmap?
Thanks for the help, Assa