<p>Hello,</p>

<p>I am using HOMER to find enriched known motifs in my differentially expressed gene lists (RNA-seq). I am using the findMotifs.pl tool. I get enriched motifs, and I would like to know now which genes have this motif. Is it possible to get these genes? I can&#39;t find it in the manual pages of HOMER, did I miss it? Does anyone has an idea how to get the target genes?</p>

<p>Ben</p>

<p>Sorry for posting this question, I found what I wanted in the manual pages section:</p>

<h3><strong>Finding Instances of Specific Motifs</strong></h3>
