Dear Noa,
Bowtie in --besthttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-bestmode 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:
galaxy-user@lists.galaxyproject.org