I am analysing Hi-C experiments and I'd like to annotate the genome (i.e. Enhancers, promoters, exons, introns, intergenic regions) in an unbiased way. I'd like to keep record, in the annotation file, of the genomic features preceding the one I am considering. For instance, discriminate in between exons following promoters and exons following introns.
Do you have suggestion on how to set this notation or suggestion of tools are mede for this purpose.