Dear all,

I have FASTQ files and on start of my read I have 7 nucleotides tag - I would like to extract reads with this specific tag.

I would like to search in first 15 nucleotides of my reads, if match - extract this read to new fastq files.

Thank you for any ideas or help.
You can also do this with BBDuk:

    bbduk.sh -Xmx1g in=reads.fq out=filtered.fq k=7 mm=f rcomp=f restrictleft=15 literal=ACGTACG

If you want multiple tags, you can list them separated by commas; and if you want to allow 1bp mismatch, set hdist=1.
