I have two ChIP-seq data, including Case and Control sample. The reads in ChIP-seq followed Poisson distribution, so how to calculate the difference and p value in peaks identified in ChIP-seq.
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I need to calculate the difference of two ChIP-seq, not one ChIP-seq and input
Please explain your experimental setting and data better in your question by editing it. What is the difference between doing case-control and case-background analysis?
Maybe, it is DiffBind what you are looking for