Matching genomic regions / Subtract BED

Description

Removes the portion(s) of an interval that is overlapped by another feature(s).

Parameters

• Minimum overlap required as a fraction of A (0.0-0.1) [0.000000001]
• Force strandedness (yes, no) [no]

Details

subtractBed searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.

Output

The output is a BED file.

References

This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

Please see the BEDTools homepage for more details.