Normally, DiffBind is used for ChIP-seq data, but I've seen it used for ATAC-seq as well. I don't see any issues with that. MACS can be used for the initial peak calling. However, when performing peak calling for ATAC-seq data, it is advised to adjust the default parameters so peaks are centered on the cutting sites. A common suggestion is `--nomodel --shift -100 --extsize 200` or `--nomodel --shift 37 --extsize 73`.
If the reads are adjusted for peak calling, what happens when I then pass the peaks and the BAMs to DiffBind? Wouldn't DiffBind quantify the peaks incorrectly since the BAMs and peaks do not really represent the same data?