Dear Noa, I also feel the same. So I think it would be better to use these three steps remove sequencing artifacts then trim the sequences by from the 5' end or if needed from the 3'end also (2-5 bases, depending on your sequence quality) finally filter the sequences by quality (I used the default parameters). Although it removed 15% of the sequences but I feel confident with the high quality data. Any better suggestion will be appreciated. CHeers, Bomba On Thu, Mar 1, 2012 at 10:48 AM, Noa Sher <noa.sher@gmail.com> wrote:

Hi

I am looking at various options of quality trimming sequences for RNA Seq analysis

I know I can chop off a certain number of bases off the 3' or 5' ends of the reads.

Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis?

Thanks

noa

___________________________________________________________ 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/

-- Dr. BOMBA DAM Alexander von Humboldt Postdoctoral Research Fellow Max-Planck-Institut für terrestrische Mikrobiologie Karl-von-Frisch-Straße 10 D-35043 Marburg, Germany E mail: bomba.dam@mpi-marburg.mpg.de PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) Assistant Professor of Microbiology Department of Botany, Institute of Science Visva-Bharati (A Central University) Santiniketan, West Bengal 731235, India. E mail: bumba_micro@visva-bhatari.ac.in, bumba_micro@rediffmail.com;