Dear Noa,

Bowtie in --best mode eliminates strand bias by forcing Bowtie to select one strand or the other with a probability that is proportional to the number of best sites on the strand.


try with this mode. I am also trying to do the same. If you find any good alternative for the whole process please let me know.

Bomba

On Thu, Mar 1, 2012 at 11:22 AM, Noa Sher <noa.sher@gmail.com> wrote:

Hi

I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks.

I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my 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;