Dear Noa,

Bowtie in 
--best<http://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-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.s...@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
>
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-- 
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....@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_mi...@visva-bhatari.ac.in, bumba_mi...@rediffmail.com;
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