HOMER motif finder, output divergent organisms

Question

[santosL]

Dear all,

I've been struggling with some problems in analyzing the output from the HOMER motif finder! I've run "findMotifsGenome.pl" command to find motifs using the bed files from my peak calling analysis. I'm doing it using E. coli data, which is causing mt the following problems:

command (pretty default): findMotifsGenome.pl peak.bed genome.fasta ./HOMER_MOTIF_Out -size 200 -mask

1. genome option: at first I was using the FASTA file for the entire genome (E. coli) as input, since it says that the new version allows you to. The problem is that once I run this, the output indicates:

   * - possible false positive 
   All the Best Match/Details similar to hsa
   

2. Then I tried to build a genome as indicated by them (http://homer.ucsd.edu/homer/introduction/update.html [3] item), which worked fine and I re-ran the findMotifsGenome.pl using the new build genome, but it returned the same output with best matches similar to human again.

Does anyone had the same issue? If so, how did you guys solved it? I've been looking for similar issues for a few days now, but couldn't find anything similar.