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
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