Hello Jiwen,

No, you do not need to join the files for the quality processing.

Hopefully this helps!

Best,

Jen
Galaxy team

On 4/9/12 9:14 AM, 杨继文 wrote:
Hi all,
I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
files. Before mapping, I need to trim the reads.

My questions is : Do I have to join pair end reads before timming, and
then split again for Tophat???

Lookiong forward to your answers.

Thanks

Jiwen




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