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
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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/