Hi Surya,

I made Galaxy scripts, FASTQ interlacer and de-interlacer, to do exactly what you are describing: https://bitbucket.org/fangly/galaxy-central/changeset/3fa11cf2730d
The tools extend the Galaxy Python API and therefore need Galaxy to work. Unfortunately, FASTQ interlacer and de-interlacer are still waiting to be committed to the Galaxy development repository by a Galaxy maintainer.

Florent

On 30/03/11 01:29, Surya Saha wrote:

Hi,

I have two fastq files with the forward(/1) and reverse(/2) paired reads. The reads are not in same order in either file, some pairs are absent/missing and the files are 8 GB each with abt 30 mill reads each.

I am trying to pull out all the paired reads for which both fwd and rev exist. Can I use a combination of fastq tools in Galaxy to do this?

Thanks!

-Surya
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