I have ChIP-Seq in a strain with defined maternal/paternal background and Now I want to use DiffBind to perform allele-specifc binding analysis. But what should be the design of analysis in this case? I can think of different ways:
- I can compare maternal ChIP vs maternal Input (group 1) to paternal ChIP vs paternal Input (group 2), In this case I will have to call peaks separately for mat/pat allele. But I am afraid that there are not enough reads to call peaks separately on alleles.
- I can compare between maternal-ChIP vs paternal-ChIP (group1) and maternal Input vs paternal Input (group 2), again by calling peaks separately for ChIP and Input.
- I can do the peak calling first on overall ChIP vs Input. Then I count the maternal/paternal reads on the peaks on both ChIP and Input samples, do differential binding using design 1 or design 2 above.
There could be other ways as well. But I would like to have some suggestions.