Question: HOMER annotatepeaks with custom genomes
gravatar for michael.law26
4.7 years ago by
michael.law2610 wrote:


I have performed annotation of my ChIP-seq data using HOMER. My experiments are performed in a yeast strain that is not the reference genome for HOMER. I uploaded my genome using the command, and everything seemed to work fine. After annotation, I wanted to make sure that the peaks corresponded to the genes that were identified. After looking in IGV, I found that my peaks were not aligned to the annotated genes.

How does HOMER compile the custom genomes? Does it use the standard reference genome as a starting point and add in my .gff data?

Anyone ever experience this or have a suggestion about how to fix it?


custom genome chip-seq homer • 1.7k views
ADD COMMENTlink written 4.7 years ago by michael.law2610
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: 1279 users visited in the last hour