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 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

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