Extracts the genomic regions in the resulting profile that are above a given threshold.

> bin/findPeaks -h

SeqCode_v1.0						User commands						findPeaks

NAME
	findPeaks - a program to find peaks in ChIPseq/RNAseq/ATACseq experiments.

SYNOPSIS
	findPeaks [-d][-l <bp>][-t <value>][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <SAM file> <name>

OUTPUT
	One folder with one file:
	- List of regions above T normalized reads.

OPTIONS
	-d : Demo mode for small BAM files (min number reads control off).
	-l : Avg. fragment size (default: 150).
	-t : Threshold for peak calling (default: 1.5).
	-w : Window resolution (default: 100).
	-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						findPeaks

Example 1. Determining the regions in the genome above 20 normalized units of H3K4me3 (ChIPseq).

> bin/buildChIPprofile -v ChromInfo.txt SRR1015741.bam H3K4me3
> bin/findPeaks -v -t 20 ChromInfo.txt SRR1015741.bam H3K4me3_T20

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]