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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
