When to use CallPeaks(), prior to merging, or after merging?

[sam-mick]

Hi there,

Just curious since it doesn't seem to be mentioned anywhere, whether peak calling using MACS3 should be done prior to merging of the data or after?

I'd assume that since it needs a common set of peaks for merging + integration that this should be done on each independent dataset - but then I noticed that it works on any given fragment files in an object, and in this vignette it's done after the UMAP is generated.

Some clarification would be much appreciated.

Thanks!