Processing and cleaning the BedGraphs generated by the MACS software.

> bin/processmacs -h

SeqCode_v1.0						User commands						processmacs

NAME
	processmacs - a program to clean MACS BedGraph profiles.

SYNOPSIS
	processmacs [-c][-v][-h]
	<chrom_info> <bedgraph.gzip> <output name> <track name>

OUTPUT
	BedGraph processed profile.

OPTIONS
	-c : Compact averaged BedGraph profile.
	-v : Verbose. Display info messages.
	-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						processmacs

Example 1. Working with the output of MACS in the UCSC genome browser.

Before, let us assume that we have run MACS to find the peaks of one sample, using a second sample as a control:

> macs14 -t H2AUb1_Pombo.bam -c ControlIP_Pombo.bam -g mm -n H2AUb1_Pombo -B -S --nomodel --shiftsize 75

MACS, after running the previous command, has generated the BedGraph profile of the ChIPseq experiment:



However, when we upload this profile in UCSC (mm9), we realize that something is wrong:



We run SeqCode for processing and cleaning this BedGraph file in mm9:

> bin/processmacs -v ChromInfo.txt H2AUb1_Pombo_treat_afterfiting_all.bdg.gz H2AUb1_Pombo_nocompact.bdg H2AUb1_Pombo

The new profile generated by SeqCode is correctly uploaded into the UCSC genome browser interface:






Example 2. Generating compact profiles that require a lower amount of space.

Now, we run SeqCode for processing and cleaning this BedGraph file in mm9 using the option -c:

> bin/processmacs -cv ChromInfo.txt H2AUb1_Pombo_treat_afterfiting_all.bdg.gz H2AUb1_Pombo.bdg H2AUb1_Pombo

When comparing to the previous profile, we see the performance of the reduction operation in the file size:



The profile generated by SeqCode is correctly uploaded into the UCSC genome browser interface:

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]