Generation of custom tracks of ChIPseq, ATACseq and RNAseq experiments for visualization in genome browsers.

> bin/buildChIPprofile -h

SeqCode_v1.0						User commands						buildChIPprofile

NAME
	buildChIPprofile - a program to generate genome-wide ChIPseq/ATACseq/RNAseq profiles for genome browser visualization.

SYNOPSIS
	buildChIPprofile [-c <Rcolor>][-d][-l <bp>][-m][-p][-s <reads>][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <SAM file> <name>

OUTPUT
	One folder with one file:
	- BedGraph profile (compressed).

OPTIONS
	-c : Track color (default: black).
	-d : Demo mode for small BAM files (min number reads control off).
	-l : Avg. fragment size (default: 150).
	-m : Invert the score of BedGraph records.
	-p : Using pair-end reads mapped in proper pair (default: single-end).
	-s : Number of spike-in reads for reference-adjusted normalization.
	-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						buildChIPprofile

Example 1: Generate the custom track of the ChIPseq experiment to be visualized in the UCSC genome browser.

> bin/buildChIPprofile -v ChromInfo.txt SRR1015741.bam H3K4me3

Example 2. Generate in higher resolution the custom track of the same ChIPseq sample.

> bin/buildChIPprofile -v -w 10 ChromInfo.txt SRR1015741.bam H3K4me3_w10

Example 3: Generate the custom tracks of the strand-specific RNAseq experiment.

> bin/buildChIPprofile -v ChromInfo.txt SRR1699465/accepted_hits_plus.bam RNAseq+
> bin/buildChIPprofile -mv ChromInfo.txt SRR1699465/accepted_hits_minus.bam RNAseq-

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]