Counting the number of ChIPseq/ATACseq/RNAseq reads on a set of genomic regions.

> bin/recoverChIPlevels -h

SeqCode_v1.0						User commands						recoverChIPLevels

NAME
	recoverChIPLevels - a program to determine the ChIPseq/ATACseq/RNAseq avg/max/total counts of reads in a list of regions.

SYNOPSIS
	recoverChIPLevels [-d][-l <bp>][-n][-s <reads>][-w <bp>][-v][-x prefix][-h]
	<chrom_info> <SAM file> <peaks.bed> <name> 

OUTPUT
	One folder with 1 file:
	- List of peaks + counts of ChIPseq/ATACseq/RNAseq reads.

OPTIONS
	-d : Demo mode for small BAM files (min number reads control off).
	-l : Avg. fragment size (default: 150).
	-n : Normalize using the total number of reads.
	-s : Number of spike-in reads for reference-adjusted normalization (with -n).
	-w : Window resolution (default: 10).
	-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						recoverChIPLevels

Example 1. Determining the ChIPseq levels of H3K4me3 in all the set of RefSeq transcripts in mouse.

(A) Counting the reads from the ChIPseq experiment on a set of genomic regions (gene bodies from RefSeq transcripts):

> bin/recoverChIPLevels -vn ChromInfo.txt SRR1015741.bam refGene_transcripts.bed H3K4me3

(B) Generating the profile for visualization in the UCSC browser (for visual confirmation):

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

Example 1. The Gdf3 gene:

#chr	pos1		pos2		locus		average	maximum	total
chr6	122555420	122560089	Gdf3-NM_008108	2.86	10.81	1331.70        (Max peak is 10.81)

Example 1. The Nanog gene:

#chr	pos1		pos2		locus			average	maximum	total
chr6	122657506	122664651	Nanog-NM_001289831	2.40	15.04	1717.44   (Max peak is 15.04)
chr6	122657582	122664651	Nanog-NM_028016	        2.40	15.04	1698.48
chr6	122657582	122664651	Nanog-NM_001289830	2.40	15.04	1698.48
chr6	122657582	122664651	Nanog-NM_001289828	2.40	15.04	1698.48

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]