Question: What is the difference between "" and "" in homer motif analysis?
gravatar for mikysyc2016
23 months ago by
mikysyc201670 wrote:

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 (

Analyzing genomic positions (

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!

chip-seq motf analysis • 1.9k views
ADD COMMENTlink modified 23 months ago by reskejak20 • written 23 months ago by mikysyc201670
gravatar for reskejak
23 months ago by
Michigan State University
reskejak20 wrote:

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

The alternative,, 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:

ADD COMMENTlink written 23 months ago by reskejak20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1592 users visited in the last hour