Question: What should I choose to best specify background sequences when looking for motifs under peaks in Homer?
gravatar for a.rex
6 months ago by
a.rex190 wrote:

I have a file with a set of intervals (corresponding to ATAC peaks) that are within introns or close to a specific type of gene (i.e. stem cell genes). I have another file of intervals for peaks that are within introns or close to another type of gene (i.e. genes expressed in the liver). I wish to look at the motifs under these two different peak sets? But what should I specify as background for homer? Can I for example give exons? Or look at motifs specific to one gene type and give it the peaks of the other gene type as background?

homer • 217 views
ADD COMMENTlink written 6 months ago by a.rex190
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: 1390 users visited in the last hour