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 > > ___________________________________________________________ > 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....@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;
___________________________________________________________ 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/
