cluster_bedpe

Concepts

A loop is a connection between two regions in the linear genome that are brought close together in 3D space. Overlapping interactions occur when loops share anchoring regions on the diagonal. cluster_bedpe groups overlapping interactions. Creating clusters from overlapping interactions provides a flexible, context-specific view of genome organization, capturing dynamic regulatory relationships that TADs may miss.

cluster_bedpe is often used after extracting loops from a .hic file with extract_bedpe.

Input

Output

Flank

Usage

cluster_bedpe clusters bedpe rows based on basepair intersections

Usage and Option Summary

cluster_bedpe -P file.bedpe

Required

Short Option	Long Option	Description
-P	--bedpe	Path of the bedpe file you want to use

Optional

Short Option	Long Option	Description
-F	--flank	Genome distance in bp to increase the size of bedpe rows. Default is 0
-h	--help	Help message