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 j...@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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