ATAC-seq peak annotation and downstream analysis I have 7 different cell types, 4 normal cell types and 3 disease cell types. 
I have done until peak calling. Now I want to do peak annotation.

The sample I have is all biological replicates. Should I merge the peak file and then do peak annotation, or should I be doing individual peak annotation?
The way we do this (and I think its quite common?), is to merge all the files of the same condition (taking the same number of reads from each), and then calling peaks on the merged sample - so you would have two peak sets - one from normal and one from disease. You then do the union of the two peak sets. 

This makes annotation much easier.

For downstream quantitative analysis, you can then quantitate each individual sample against the merged peak set.