Calculation of the overlap between peaks of two different ChIPseq samples.

> bin/matchpeaks -h

SeqCode_v1.0						User commands						matchpeaks

NAME
	matchpeaks - a program to compare 2 lists of peaks/regions.

SYNOPSIS
	matchpeaks [-l <bp>][-v][-x prefix][-h]
	<peaksA.bed> <peaksB.bed> <nameA> <nameB>

OUTPUT
	One folder with 3 files (BED): common in both, only in A, only in B.

OPTIONS
	-l : Minimum overlap size (default: 1).
	-v : Verbose. Display info messages.
	-x : Prefix for the output folder.
	-h : Show this help.

SEE ALSO
	SeqCode homepage: http://ldicrocelab.crg.es
	GitHub source code: https://github.com/eblancoga/seqcode

AUTHORS
	Written by Enrique Blanco.

SeqCode_v1.0						User commands						matchpeaks

Example 1. Matching two sets of peaks with all the classes of overlap.

> bin/matchpeaks -v A_peaks.bed B_peaks.bed A B

	Peaks intersected in A: 2/3 (66.67%)
	Peaks intersected in B: 2/3 (66.67%)
	Peaks non-intersected in A: 1/3 (33.33%)
	Peaks non intersected in B: 1/3 (33.33%)

UCSC genome browser screenshot:

Please, follow the link below for further information on how to get and preprocess the raw data of published ChIPseq and RNAseq samples utilized in this glossary of SeqCode functions.

[SAMPLES]