I am planning to use exogenous chromatin as a spike in control with my actual sample from mouse to perform ChIP-seq for peak calling and differential binding analysis for histone modifications. this involves down-sampling the uniquely mapped read files to the calculated normalization factor from the spike in. This is generally helpful for peak calling and visualizing in IGV browser. But I have not found any reference on whether it is considered in differential binding analysis. Also, nothing is mentioned in the Diffbind vignette. Could you please explain how this strategy might affect using the diffbind package?
I greatly appreciate your time to read and answer to my question! Thank you in advance!