Hi Joanna,
During trimming, some of the reads may be removed from your dataset. Depending on what you need to do, you may or may not want to discard reads that don't have a "mate" mate anymore. If so, you might consider using the FASTQ de-interlacer and interlacer tools.
Florent

On 26/10/11 02:52, Kuehn, Joanna S [V MPM] wrote:

Hello,

I was wondering, can Galaxy’s FASTQ Quality Trimmer tool be used on Illumina paired-end data? Would the forward and reverse read files need to be processed separately and be un-joinable afterwards for filtering?

Thank you,

Joanna
___________________________________________________________
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/