Well, you could do something like this:
Code:
for j in *reads.fq; do deinterleave_fastq.sh < $j $(basename $j .fq).F.fq $(basename $j .fq).R.fq [compress]; done
Best,
Matt.
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for j in *reads.fq; do deinterleave_fastq.sh < $j $(basename $j .fq).F.fq $(basename $j .fq).R.fq [compress]; done
for j in *fastq; do deinterleave_fastq.sh $j *options; done
deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
for j in *fastq; do deinterleave_fastq.sh $j *options; done
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