Peak Analysis

Useful peak manipulation (filter, comparison, and simulation) utilities.

Tool Name	Input	Output	Description
peak-align-ref	BED(ref) + BED(peak)	CDT	Align BED peaks to Reference BED file creating CDT files for heatmap generation.
filter-bed	BED	BED(cluster) + BED(filter)	Filter BED file using user-specified exclusion zone using the score column to determine which peak to retain.
tile-genome	genomeName	[BED|GFF]	Generate a coordinate file that tiles (non-overlapping) across an entire genome.
rand-coord	genomeName	[BED|GFF]	Generate a coordinate file that tiles (non-overlapping) across an entire genome.
signal-dup	GFF + BAM	TXT	Calculate duplication statistics at user-specified regions.
sort-by-dist	BED/GFF	BED/GFF	Sort BED/GFF by distance to another BED/GFF (e.g. peak annotations).