Gene names from mixed location BED file

Question

[rbronste]

Wondering if anyone has a handy script for parsing out gene/isoform names from a bed file which contains varied genomic intervals, with ~80% falling within the promoter region as defined +/- 2kb of TSS? Thanks!

[ATpoint]

Check the options -F and -f which can be used to define minimum fractions of overlaps in bedtools intersect.

[rbronste]

We no the BED file only contains the intervals and not the gene names themselves.