I'm a bit of a scripting novice and would greatly appreciate some advice. I have fastq read files from numerous sequenced ddRAD libraries and on which I'd like to perform in silico digests (using MseI: A^ATT) and retain all fragments greater than a certain length. The output needs to be in fastq format for downstream processing. I'm able to do something like this using the Bio.Restriction package of Biopython, but the output is fasta (i.e., there's no read quality data). Does anyone have an idea on what a suitable approach would be?
Many thanks in advance.