I am currently analyzing ChIP-seq data and am using HOMER to analyze my peak file. I am wondering if there is any way I can prioritize protein-coding genes.
The reason I am asking is one of the peaks from my IP is around 1.5kb upstream of a gene. The protein we are looking at is known to promote this gene's expression. However, the annotatepeak.pl function says this peak is a long noncoding RNA.
Does anyone know if I can prioritize this peak annotation to ensure protein-coding is called before long noncoding RNA?
I am using Arabidopsis as a model organism if anyone has any references to use.