Question: Find genes of enriched known motif results in HOMER
2
gravatar for b.nota
2.9 years ago by
b.nota5.0k
Netherlands
b.nota5.0k 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 • 2.5k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by b.nota5.0k
2
gravatar for b.nota
2.9 years ago by
b.nota5.0k
Netherlands
b.nota5.0k wrote:

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

Finding Instances of Specific Motifs

ADD COMMENTlink written 2.9 years ago by b.nota5.0k
1
gravatar for b.nota
2.9 years ago by
b.nota5.0k
Netherlands
b.nota5.0k 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 2.9 years ago • written 2.9 years ago by b.nota5.0k
0
gravatar for rlbowman88
2.9 years ago by
rlbowman880
United States
rlbowman880 wrote:

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

ADD COMMENTlink written 2.9 years ago by rlbowman880
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