Question: Motif location for enriched motif in HOMER
0
gravatar for Prakash
21 months ago by
Prakash1.9k
India
Prakash1.9k wrote:

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.

chip-seq next-gen • 1.0k views
ADD COMMENTlink modified 20 months ago by genomax83k • written 21 months ago by Prakash1.9k
2
gravatar for Kevin Blighe
20 months ago by
Kevin Blighe59k
Kevin Blighe59k wrote:

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

ADD COMMENTlink written 20 months ago by Kevin Blighe59k

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.

ADD REPLYlink written 20 months ago by Prakash1.9k
1

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

ADD REPLYlink written 20 months ago by Kevin Blighe59k
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