Question: Re: Filtering Reads On Wrong Strand Before Fpkm Scoring On Cufflinks
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Bomba Dam • 40 wrote:
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
--
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;