serious question. When one runs motif enrichment analysis, I think it is generaly desirable to know which specific peaks were found to have a motif. Why does a tool like HOMER's FindMotifsGenome.pl not report every instance of where each motif was found, and one must run a whole different tool for that task? Is this a feature more people would wish for?

#genomics #bioinformatics #atacseq #chromatin #motifs #computational #compbiology