I am looking at the ENCODE ATAC-seq pipeline: https://www.encodeproject.org/pipelines/ENCPL035XIO/

They have two different steps:

 - "call nuclease accessible regions using FSeq" (in PDF) or "open chromatin region identification" (on diagram)
 - "call nuclease accessible peaks using Homer" (in PDF) or "peak calling" (on diagram)

Regardless of the tool used, what is the difference between "regions" and "peaks"? I would think those are the same thing (in this context, a set of loci where the reads accumulate).

I received a very helpful clarification after emailing ENCODE directly:

> Nuclease accessible regions tend to be long, e.g. 10 kb or longer.
> This was clear even in the early papers on DNase sensitivity
> (mid-to-late 1970's; Groudine and Weintraub). These accessible regions
> can contain entire genes or even clusters of genes. Within the
> nuclease accessible regions, some localized DNA segments are so
> readily cleaved that double-strand breaks are generated at that
> position in a substantial fraction of the cells in the population.
> These are the DNase-hypersensitive sites (DHSs) first mapped by Carl
> Wu (late 1970's). I see the Fseq "regions" as the equivalent of
> nuclease accessible regions, and the Homer "peals" as the equivalent
> of DHSs.
> 
> If you look at the signal track for DNase-seq or ATAC-seq, you see
> broad regions of signal that are significantly above the background.
> Within those regions, you see localized peaks, often many peaks per
> region. Fseq calls the broad regions, and we use Homer to call the
> localized peaks. MACs can be used for peak calling as well, Anshul
> Kundaje is doing that. You can see similar analyses in the work from
> John Stamatoyannopoulos for DNase-seq. I think Hotspots are like
> regions, and DHSs are peaks confined to a defined length.


