Hi

as C: Every time the results of findMotifGenome.pl in HOMER is different mentioned, I found everytime I run HOMER, the result is different. I find it seems there is no function about specifically choosing background in HOMER. So I am wondering whether I can set my background file to fix my result when analysising ChIP-Seq peak.

And I may only have one peak file, which means I do not set another peak file as background file like HOMER said

Specify peaks common to two cell types as background when trying to find motifs specific to a set of cell-type specific peaks - this will help cancel out the primary motif and reveal the co-enriched motifs