[BioC] package to count read prior to DESeq?

[Steve Lianoglou]

Hi Nathalie,

On Fri, Feb 3, 2012 at 10:39 AM, nathalie <nac at sanger.ac.uk> wrote:
> Hi,
> Is there a package to create a count table from bam files, which gives an
> output compatible with DESeq analysis?

The summarizeOverlaps function in the GenomicRanges library is
probably a good place to start.

HTH,
-steve

-- 
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