chromatin loop annotation for hic

Question

[J.F.Jiang]

Hi all,

We had discovered neoloops from hi-c data, either from intra or inter chromosomes.

Chrom regions were listed as chrom, start, end in output bed files.

To further investigate the contacts of the regions, we aimed to annotate the region to discover the detailed contacts, such as ehancer-promoter interaction or others.

Is there any existing tools that can directly annotate the bed regions?

Best, Junfeng

[ATpoint]

Do you have the resolution to connect E-P pairs? I mean, essentially it comes down to an intersection operation between the ranges of known promoters and the coordinates of the enhancers within the looping domains. bedtools intersect as a command line interface or GenomicRanges or plyranges in R come to mind.

[J.F.Jiang]

YES, using bedtools or GRanges can map the genomic region to promoter regions. However, it seems that the enhancer or super-enhancer regions are quite tissue or cell-type specific.

Or is there any well reviewed enhancer database that can be used to annotate the regions?