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

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