Thread: NGS users
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Old 04-28-2014, 03:41 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

That's an annoying format that you have to deal with. You can split each line and output things in fastq format with:

awk -F ":" '{printf("@%s:%s:%s:%s:%s\n",$1,$2,$3,$4,$5);print $6; print"+"; print $7}' foo.txt > foo.fastq
You'll need to rename "foo.txt" to whatever your files are actually called.
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