[BioC] DEseq for chip-seq data normalisation

Rory Stark Rory.Stark at cruk.cam.ac.uk
Wed Nov 6 12:32:07 CET 2013

Hi Guiseppe-

I'm not sure why you want to downsample? The normalization is supposed to
take care of differences in read depth and distribution of read densities
amongst peaks.

edgeR/DESeq/DESeq2 do calculate overall scaling factors for each library
as part of the normalization computation, so it may be useful to retrieve
those to see how each library is being weighted. This would be better than
basically reverse-enginering it by calculating the ratios between the
original values and the normalized ones.


>Date: Wed, 06 Nov 2013 10:48:56 +0000
>From: Giuseppe Gallone <giuseppe.gallone at dpag.ox.ac.uk
>Thanks a lot Rory. Do you think it would then make sense to use the
>normalised counts in the peaks to build a ratio based on the raw count
>and then feed this ratio to, say, picard to get a downsampled bam from
>the original bam?

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