how to calculate p value

Question

[Ben]

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.

[Michael]

Hello Ben!

Questions similar to yours can already be found at:

• Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. genome average)
• Calculating p-Value for an observed/expected Ratio

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

[Ben]

I need to calculate the difference of two ChIP-seq, not one ChIP-seq and input

[Michael]

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?

[e.rempel]

Maybe, it is DiffBind what you are looking for