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

Hello,

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 loadgenome.pl 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 • 1.5k views
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