I used
bioawk -cfastx 'length($seq) > 1 {print "@"$name"\n"$seq"\n+\n"$qual}' in.fq.qz | gzip > out.fq.qz
in order to keep a particular read length, but this command shortened the header from
@A00199:161:HF3JLDMXX:1:1101:5882:1063 2:N:0:CTGTAGCC+GAACAGGC
to
@A00199:161:HF3JLDMXX:1:1101:5882:1063
How is it possible to fix the bioawk command to remain the full command?
{print "@"$name " " $comment"\n"$seq"\n+\n"$qual}– user977828 Sep 06 '18 at 04:04