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?