[BioC] Fwd: differential binding question

[Heidi Dvinge]

Dear Mali.

> Dear Users
> We have RNA-IP-seq for two conditions with two biological replicates each.
> So in total we have 8 samples:
> 2 for condition1 IP
> 2 for condition1 Input
> 2 for condition2 IP
> 2 for condition2 Input
> We would like to find differential binding between the two conditions

You might want to have a look at DiffBind, one of the new packages in the
latest Bioconductor release. It's designed for differential binding
analysis of ChIP, but can probably also be used for RNA-IP. AFAIK, it uses
some of the funcitonalities from edgeR and DESeq.

HTH
\Heidi

> which
> are not influenced from differences in gene expression (Input samples are
> actually regular RNA-seq).
> I thought of first finding peak regions (maybe by pooling all IP and all
> Input samples) and run ChIP-seq peak caller, count how many reads fall
> within these regions in each of the samples, and then run DESeq and edgeR
> in order to find differential binding.
> Is this can be done with edgeR and DESeq (again the Input is different for
> the two conditions, and we would like to cancel out differential gene
> expression)?
> Thanks
> Mali
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>