[Bioc-sig-seq] differential binding

[Mark Robinson]

Hi Bogdan,

Short answer is yes, you can use edgeR or DESeq in a differential binding
context, as long as you can represent your regions as a table of counts;
we and several others do exactly this.  As with RNA-seq, there are various
ways to arrive at a table of counts.  For example:
https://stat.ethz.ch/pipermail/bioconductor/2011-July/040409.html

Regards,
Mark


> Dear all,
>
> please could you advise me on the following : could someone use the
tools
> that are developped for assesing differential expression in RNA-seq,
(edgeR, DESeq), in a Chip-Seq context, namely measuring differential binding
> of a protein across multiple genome regions ? thanks a lot,
>
> Bogdan
>
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