I called 90,112 peaks from H3K27ac CHIP-seq data using MACS2, and then identified 1,108 super enhancers (SEs) using ROSE with default parameter '-s 12500 -t 2500'. However, I found that most of SEs are located in promoter regions.
The genomic annotation of 1,108 SEs by ROSE:
The genomic annotation of 90,112 peaks by MACS2:
I am kind of interested in SEs located in distal intergenic regions. But now the number of this type of SEs is limited. Could any one guide me to solve this problem? Any suggestion will be highly appreciated. Thank you in advance.