Depleting BED file of specific regions

Question

[rbronste]

Hi,

Wondering about the best/easiest way to deplete a BED file of regions that are promoter proximal - or any other specific genomic "region"? Thanks

Rob.

Answer 1

[Pierre Lindenbaum]

bedtools intersect http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[rbronste]

So you would just use the intersect of BED file of promoter distal regions for lets say mm10? Thanks.