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Hello Ben!
Questions similar to yours can already be found at:
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!
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