Combination/subtraction of two ChIPseq/ATACseq/RNAseq experiments for visualization in genome browsers.

> bin/combineChIPprofiles -h

SeqCode_v1.0						User commands						combineChIPprofiles

NAME
	combineChIPprofiles - a program to combine two genome-wide ChIPseq/ATACseq/RNAseq profiles.

SYNOPSIS
	combineChIPprofiles [-c <Rcolor>][-d][-l <bp>][-m][-p][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <SAM file1> <SAM file2> <name1> <name2>

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).
	-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						combineChIPprofiles

Example 1. Subtracting the Input from a ChIPseq experiment.

> bin/buildChIPprofile -v ChromInfo.txt SRR1015741.bam H3K4me3
> bin/buildChIPprofile -v ChromInfo.txt SRR953585.bam Input
> bin/combineChIPprofiles -v ChromInfo.txt SRR1015741.bam SRR953585.bam H3K4me3 Input

Example 2. Combine RNAseq (strand-specific) into a single track.

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