What is the difference between "findMotifsGenome.pl" and "findMotifs.pl" in homer motif analysis?

Question

[mikysyc2016]

Hi all, Did you try both of them to see what is the difference between these two to do motif analysis with ChIP-seq results? Homer said:

Analyzing lists of genes with promoter motif analysis ( findMotifs.pl)

Analyzing genomic positions ( findMotifsGenome.pl)

After Peakcalling, I want to do motif analysis, so which one I can use?

If I get a peak, and I want to extract the sequence of that single peak and to see whether and how many certain motif in it, how I can do that? Can you give me some suggestion?

Thanks in advance!

Answer 1

[reskejak]

The answer lies within your own explanation! You will want to use findMotifsGenome.pl by supplying a HOMER-ized BED file (see manual). This will identify enriched motifs from the ChIP peaks you empirically determined.

The alternative, findMotifs.pl, is useful for seeking underlying regulatory patterns when all you have is a list of genes, e.g. RNA-seq output. Annotating peaks to a nearby gene would also permit this analysis, but you're losing the strong experimental evidence obtained from your ChIP data. If you have direct coordinates, which you predict are functional by some assay, then you will want the most robust analysis from these specific coordinates: findMotifsGenome.pl.