Question: Find genes of enriched known motif results in HOMER
2
gravatar for Benn
4.2 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

Hello,

I am using HOMER to find enriched known motifs in my differentially expressed gene lists (RNA-seq). I am using the findMotifs.pl tool. I get enriched motifs, and I would like to know now which genes have this motif. Is it possible to get these genes? I can't find it in the manual pages of HOMER, did I miss it? Does anyone has an idea how to get the target genes?

Ben

rna-seq motif homer • 3.9k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Benn7.9k

Can you please point me to the relevant part of the manual? I had the same question in mind.

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 4.2 years ago by rlbowman880
2
gravatar for Benn
4.2 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

Sorry for posting this question, I found what I wanted in the manual pages section:

Finding Instances of Specific Motifs

ADD COMMENTlink written 4.2 years ago by Benn7.9k
1
gravatar for Benn
4.2 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

If you go to:

http://homer.salk.edu/homer/microarray/index.html

You'll have to scroll down to: Finding Instances of Specific Motifs

You need the motif file from your analysis and the same settings, good luck!

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Benn7.9k
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