I would be really grateful for your advice in this regard. In Chip-Seq where there are all 3 IP, Input and Mock how to get the best peak calls.
- To run IP vs Mock and get peak calls
- To have two runs IP vs Input and Mock vs Input and cancel out the peaks in mock with either bedtools or diffBind.
My hunch and preference would be the second one. As mock is not a random sample from genome and I presume peak callers would need a random sample in control. The fingerprint plots of Mock clearly indicate a diffuse but substantial enrichment similar but less than IP. Also there could be loss of power if (again I presume) if both case and control have enrichment.
I am using the Encode Chip-Seq pipeline and I don't think mock and input can be incorporated together with IP in one go.
So Many Thanks!