Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)

Question

[a.rex]

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?

Answer 1

[Jingyue]

You can use Csaw (https://bioconductor.org/packages/release/bioc/vignettes/csaw/inst/doc/csaw.html) it use window-based method for differential binding analysis and can avoid using peaks from MACS2.