I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings.
Is there any good tools to annotate these broad peaks to coding genes?
I know GREAT(http://great.stanford.edu/public/html/) is a wonderful tool for narrow peak annotation such as ATAC or H3K27ac.
Since broad peaks span across multiple genes or gene deserts, I was wondering any standard way to annotate these peaks.
Any suggestion, or some example reference paper will also be helpful.
Thank you very much in advance.