So I've been using HOMER to perform motif enrichment analysis in a set of regions (BED file) and I'm getting nice enriched motifs. I think the output of findMotifsGenome.pl is fine, but I'm struggling to make a final analysis.
I would like to know which motifs are present in which regions. I have seen in some papers where they report the different motif instances in the different regions.
I'm sure it's easy enough to do that but I cannot find how to do it. How could one determine the instances of the motfis present at the regions, I guess coming from the output .motif files from findMotifsGenome.pl