I'm relatively new to bioinformatics, so sorry if this question sounds silly!
I have started to use Homer to find a specific motif in a list of genes.
The matter is: when I run findMotifsGenome.pl using -find <motif file> , I only a couple of genes from my list seem to contain the motif.
However, when I run annotatePeaks.pl with -m <motif> I get a massive excel table in which each gene seems to contain the motif multiple times.
From what I understood, the output should be the same in both cases... am I missing something? Thanks in advance to everyone who will help! :)