Intersecting unbalanced BED files, normalizing for one

Question

[LacquerHed]

Have two bed files I am intersecting, one of approximately 500 promoters +/- 2kb of TSS and the other some locations of histone marks within those promoters. There are many more intervals in the latter dataset, I would like to get the number of intersects that are unique to the promoter interval file, meaning that even if 25 intervals from the histone mark fall within one promoter I would like it to report 1 intersect. Maybe there is some way of merging across those 25 and making one unified interval that stretches across them. Not really sure of a good way to go about this, thanks.

[Jianyu]

you can use bedtools intersect with -wa option to report the intersected promoter for each interval, then use sort -u to get the unique promoter entry