[BioC] package to count read prior to DESeq?

[Wei Shi]

Dear Natalie,

The featureCounts function in Rsubread package can summarize read counts for genes or exons (each read will be assigned to at most one exon if reads are summarized to exon level). It uses the NCBI annotation for read summarization, but you can provide your own annotation as well.

This function is very quick. It only takes a couple of minutes to summarize 10 million reads.

Hope you will find it useful.

Cheers,
Wei


On Feb 4, 2012, at 2:39 AM, nathalie wrote:

> Hi,
> Is there a package to create a count table from bam files, which gives an output compatible with DESeq analysis?
> thanks
> Nat
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered ...{{dropped:18}}