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dpryan · 04-28-2014, 03:41 AM

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

Code:

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.

04-28-2014, 03:41 AM	#2
dpryan 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: Code: 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.