Motif location for enriched motif in HOMER

Question

[Prakash]

Hi,

A quick question, why homer gives different number of regions for a given motif when extracting motif location using findMotifsGenome.pl and annotatePeaks.pl

e.g from HOMER tutorial

findMotifsGenome.pl ERalpha.peaks hg18 MotifOutputDirectory/ -find motif1.motif > outputfile.txt

annotatePeaks.pl ERalpha.peaks hg18 -m motif1.motif > outputfile.txt

If I analyze for my peaks for a given motif , I get different no. of total regions having this motif.

Answer 1

[Kevin Blighe]

Just on face value, the programs have different functionality, so, I would not expect them to produce the exact same results.

annotatePeaks.pl is about annotating already-identified peaks with current knowledge.

findMotifsGenome.pl is specifically about "discovering motifs in ... genomic regions". One clear distinction that I see is that findMotifsGenome.pl specifically states that it will search for novel motifs.

There are undoubtedly other subtle differences in the command line parameter settings.

Kevin

[Prakash]

Thanks Kevin !

Actually I performed de novo motif analysis of peaks using findMotifsGenome.pl and it showed enrichment for a motif, say 20 % of total target. I was interested to know the genomic regions for this enriched motif. So I used findMotifsGenome.pl to extract the regions and it extracted genomic regions more than 20% whereas annotatePeaks.pl extracted ~20 % of total peaks.

[Kevin Blighe]

Perhaps you could look at some individual examples of where they differ. Then, you may better understand in which way(s) the 2 functions behave differently