in silico restriction digest of Illumina reads (fastq file)

[berthold]

Hi

I wonder whether anyone has a solution for a restriction digestion script that works on fastq files (Illumina reads), splitting any reads that contain the restriction site into two separate reads (and writing it back into the fastq file)?

Actually I am not so much interested in restriction as such - I have reads from co-ligated and nebulized PCR fragments, so I'd like to separate those reads at the ligation junctions, and I thought I could tweak a restriction script (preferentially, Perl) into doing that.

Any hints appreciated.

regards,
Berthold

[gholmes]

Hi Berthold,

Did you ever find a solution to doing in silico digestion of fastq files and writing output back into fastq format files? I've been trying to do this with the Bio.Restriction module of BioPython, but the output is fasta (with read quality data being lost).

Regards,
Gareth

[berthold]

Thanks for the hint Gareth.
No I did not find a way to do it otherwise yet (but it wasn't high priority). There's a student in my group now who is good with Python, I'll consult with him.

best regards,
Berthold