[Bioc-sig-seq] Alignment to only 1 direction DNA strand

[Steve Lianoglou]

Hi,

On Tue, Jul 6, 2010 at 8:56 PM, Lana Schaffer <schaffer at scripps.edu> wrote:

> Hi,
> We have directional inserts to sequence (Illumina platform) and want to align
> to either the sense or antisense strand of DNA one at a time.  Is there
> alignment software to do this?

I know that bowtie can do this (I'm guessing BWA can as well).

Look for the description of the --nofw and --norc arguments here:
http://bowtie-bio.sourceforge.net/manual.shtml

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact