I'll add that the reference data for ROSE hasn't been updated since like 2012, and it really shows. I've found it worth the effort to munge a more recent annotation into the refflat format and slap it into the annotation directory/alter source code as necessary.

Additionally, it has some hidden parameters that aren't accessible without altering source code that lead to unclear behaviors during loci stitching (e.g. a region that spans 3 TSS elements won't be stitched together). This results in certain loci looking like super enhancers without being identified as such. Again, not much you can do without dorking with the source code, but just be aware of it.

How can I obtain the annotation file? I have a peak file of enhancers; can I simply use it as a GFF file?