Jiwen, I wonder if you are thinking about the situation where you could be discarding reads that are to short after trimming?. In that case you could be getting the two files out of sync. If this is the case, I think you do need to join the files first, do the trimming and then take them apart again. Regards, Carlos On Mon, Apr 9, 2012 at 1:25 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

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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