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.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

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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.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;