SeqCode: combineChIPprofiles

General description

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

> bin/combineChIPprofiles -h

SeqCode_v1.0						User commands						combineChIPprofiles

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

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

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

	-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.

	SeqCode homepage:
	GitHub source code:

	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-

ChIPseq and RNAseq samples

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.