I am using HOMER to analyse Hi-C data of Hordeum vulgare (Barley). I have computed the significant chromatin interactions and now I want to annotate these interactions. HOMER doesn't have an inbuilt genome of barley in it, so, I am not able to annotate the interactions. I tried using GFF and GTF file, but it is not working.
Can anyone suggest me how to annotate chromatin interactions? Is there any tool available for this?