hi Rushiraj,

The DESeq/DESeq2 model takes care of differences in library size through
estimation of a size factor, s_j in Equation (2) in the paper here
http://genomebiology.com/2010/11/10/r106

See the manual page ?estimateSizeFactors for DESeq/DESeq2.

Mike


On Thu, Oct 17, 2013 at 11:38 AM, Rushiraj Manchiganti
<rushirajm@gmail.com>wrote:

> Hi,
>
> I have got a set of RNA-seq data with the control sample having around 8
> million reads and the treated samples in the range of 13-17 million reads.
>  I was wondering if DESeq can handle this kind of difference in number of
> reads between samples?  Or a down sampling of reads is necessary before
> DESeq?
>
> Regards,
>
> Rushiraj
>
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