Question: Motif location for enriched motif in HOMER
gravatar for Prakash
2.1 years ago by
Prakash1.9k wrote:


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

e.g from HOMER tutorial ERalpha.peaks hg18 MotifOutputDirectory/ -find motif1.motif > outputfile.txt 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 • 1.2k views
ADD COMMENTlink modified 2.0 years ago by genomax89k • written 2.1 years ago by Prakash1.9k
gravatar for Kevin Blighe
2.0 years ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

Just on face value, the programs have different functionality, so, I would not expect them to produce the exact same results. is about annotating already-identified peaks with current knowledge. is specifically about "discovering motifs in ... genomic regions". One clear distinction that I see is that specifically states that it will search for novel motifs.

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


ADD COMMENTlink written 2.0 years ago by Kevin Blighe65k

Thanks Kevin !

Actually I performed de novo motif analysis of peaks using 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 to extract the regions and it extracted genomic regions more than 20% whereas extracted ~20 % of total peaks.

ADD REPLYlink written 2.0 years ago by Prakash1.9k

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 2.0 years ago by Kevin Blighe65k
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