Not the most convenient solution, but what I normally do in this situation
is to combine the two files, filter then split again. There are tools for
combining and splitting paired fastq files in Galaxy.

Hope it helps,
Carlos
On Jan 8, 2013 12:55 AM, "柴田 弘紀" <hshib...@gen.kyushu-u.ac.jp> wrote:

> Hi there,
>
> I obtained two fastq files from GA paired end run. I filtered each file by
> quality using fastq tool kit. Then some forward reads may be removed by low
> quality whereas the reverse counterparts are OK to be remained on the other
> file, or vice versa.
>
> I want to remove those "unpaired" reads from filtered fastq files so that
> the two new fastq files contain the identical sets of the reads.
>
> Is it possible to do it on galaxy?
>
> Thank you very much.
>
> Hiroki
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