Question about the use of NucleoATAC.

[chesterlee7246]

Hi!@AliciaSchep, I simply want to get nucleosome position from MNase-seq data using NucleoATAC. But I don't understand 3rd Necessary Files:

3. Sorted bed file with regions for which nucleosome analysis is to be performed. These regions will generally be broad open-chromatin regions (i.e. regions called by MACS2 with the --broad flag). It is potentially advisable to extend these regions a bit (e.g. using bedtools slop). Regions should not overlap so it is advisable to use bedtools merge on these regions.

What command should i use? Thanks!