Match peaks and target genes depending on the location of both sets of coordinates.

> bin/matchpeaksgenes -h

SeqCode_v1.0						User commands						matchpeaksgenes

NAME
	matchpeaksgenes - a program to match peaks to genes.

SYNOPSIS
	matchpeaksgenes [-udUDse <value>][-v][-h]
	<peaks.bed> <refGene.txt>

OUTPUT
	List of matches (STDOUT). Each line is a peak associated to a transcript.

OPTIONS
	-u : Use X bp upstream of the TSS, including gene body.
	-d : Use X bp downstream of the TES, including gene body.
	-U : Use X bp upstream of the TSS, excluding gene body.
	-D : Use X bp downstream of the TES, excluding gene body.
	-s : Use only +/- X bp around the TSS.
	-e : Use only +/- X bp around the TES.
	-v : Verbose. Display info messages.
	-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						matchpeaksgenes

Example 1. Matching peaks within the promoter (2.5 Kbp upstream of TSS) and the body of mouse genes.

> # Full output: peaks and genes
> bin/matchpeaksgenes -v -u 2500 H3K4me3_peaks.bed refGene.txt > H3K4me3_RefSeq_output.txt

> # List of target genes
> bin/matchpeaksgenes -v -u 2500 H3K4me3_peaks.bed refGene.txt | gawk '{print $5}' | sort | uniq > H3K4me3_RefSeq_target-genes.txt

> # Custom tracks for UCSC genome browser
> gawk 'BEGIN{OFS="\t"; print "track name=overlap_peaks color=200,100,0";}{print $1,$2,$3,$4}' H3K4me3_RefSeq_output.txt > H3K4me3_RefSeq_PEAKS.txt
> gawk 'BEGIN{OFS="\t"; print "track name=overlap_genes color=0,100,0";}{print $7,$9,$10,$5"-"$6}' H3K4me3_RefSeq_output.txt > H3K4me3_RefSeq_GENES.txt

UCSC genome browser screenshot:



Example 2. Matching peaks within the promoter (excluding the body of target genes).

bin/matchpeaksgenes -v -U 2500 H3K4me3_peaks.bed refGene.txt > H3K4me3_RefSeq_2_output.txt		     

UCSC genome browser screenshot:



Example 3. Matching peaks within +/- 500 bps around the TSS.

bin/matchpeaksgenes -v -s 500 H3K4me3_peaks.bed refGene.txt > H3K4me3_RefSeq_3_output.txt

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]