need to deinterleave/split all fastq files within a directory

[lac302]

I've been using this script in the link below for several years when I need to split PE reads into separate R1 and R2 files.

https://gist.github.com/nathanhaigh/3521724

Does anyone know of a way to do the same thing recursively to a whole folder? I have 200 RNAseq samples that all need to be split.

[neavemj]

Maybe you could loop over each of the interleaved files and run the script? Something like:

for j in *fastq; do deinterleave_fastq.sh $j *options; done

If you could tell me your directory structure and the command for how you normally run the program, I could be more specific.

Cheers,

Matt.

[lac302]

Maybe you could loop over each of the interleaved files and run the script? Something like:

for j in *fastq; do deinterleave_fastq.sh $j *options; done

If you could tell me your directory structure and the command for how you normally run the program, I could be more specific.

Cheers,

Matt.

deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]

The directory structure is just a folder of interleaved fastq files *0001reads.fq, *0002reads.fq, etc.

[neavemj]

Hi lac302,

Well, you could do something like this:

for j in *reads.fq; do deinterleave_fastq.sh < $j $(basename $j .fq).F.fq $(basename $j .fq).R.fq [compress]; done

It's still a bit tricky to tell without seeing the full file name, or understanding completely how the program works, but I think this should do the job.

Best,

Matt.