I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS2, but I found that there are some differences in shift size (plus or minus direction). I like to know which one is better for either ATAC-seq or DNase-seq
(e.g. --nomodel --shift -100 --extsize 200 or --nomodel --shift 100 --extsize 200). is it right that because most accessible regions in ATAC-seq and DNase-seq located in 5' region so using
--shift -100 is recommended?