I am new to DESeq, so apologies if this is a simple question!

I am planning to use DESeq to compare ChIP-seq sample binding regions, but i am wondering what the best method of running DESeq might be.  I have several thoughts about
this, what would you suggest?  The initial problem i see is that the binding regions have different length coordinates and so do not initially make discrete entities like gene in RNA-seq.

a) Take the binding region coordinates for sample A and count the number of reads that fall into those coordinates for both samples A and B and run DESeq. Then do the same with coordinates with sample B regions and run DESeq again.

b) Merge the binding regions of samples A and B and run DESeq once.  This way overlapping binding regions would be merged into one representative region, and if there was a binding region in set A not present in set B it would be represented in this case.

c) Take 1000bp bins over the entire genome and count read coverage from both samples.  I guess with this method that bins with 0 counts would be rejected.

Thank you for any guidance on this.

Ian


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