I have a collection of genomic coordinates (BED file) that I have generated in an ATAC-Seq experiment. These genomic locations are annotated as distal intergenic. I have collected from publications a databases a collection of known enhancer regions in a single BED file. What I would like to do is find the overlap between my two BED files.
For that, I am using bedtools intersect. One parameter that I am not quite sure how to set uo is the command -f or the Minimum overlap required as a fraction of A (first input file). This will set with how much overlap I consider two genomic regions to present in my two input files. My question is: what is the minimum overlap to confidently say there is an overlap? Any thoughts or recommendation?