I have 2 conditions under which I performed ChIP, each with 3 replicates. I want to perform differential binding analyses between them. I generally get a coverage file using the bamCoverage tool in deep tools (with the SES method) - this allows me to visualise my ChIP signal tracks and compare. But I really want to get a list of regions which are different; in the past peak calling methods have not been useful as the MACS peak calling for my samples tend to be wrong and I think it is because SES is more sensitive at look at enrichment over input.
Any ideas how I can avoid using MACS but still do this DiffBind type of analysis?