Hi Everyone

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.

Some more info might help in figuring out what to do. How many separate ChIPs do you have? Do you have separate ChIPs on the maternal/paternal strands, or are you separating he maternal/paternal reads after the sequencing? How many replicates do you have of each group? How many ready for each ChIP?

In general, it should be OK to call peaks using all the reads for each ChIP, (option 3). Then you can count the reads-in-peaks separately for each condition and compare them in DiffBind. 

Cheers-

Rory

Hi Vivek-

in this case, I would call peaks for the 10 ChIPs (5TF x 2 reps), and generate two .bam, files for each ChIP (maternal/paternal). in DiffBind, the sample sheet would have 20 samples, with each ChIP having the same peak file but a different bam file. Then compare the maternal to paternal (for each TF I assume).

Cheers-

Rory