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 >> >> >> >> >> ___________________________________________________________ >> 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/ > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/