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.
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
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.
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
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