README

This pipeline will use previously aligned data and will perform those steps:
	1- Peak calling (default: macs)
	2- Annotation (R's ChIPpeakAnno)
	3- Selection of the regions in the proximal promoter

To use the pipeline:
	1- Go to the directory where you wish to store the results.
	2- Create a file named config.txt. In this file, write the name of the files to analyze.
		One (treatment only) or two (treatment and control) file per line.
	3- Call the init script situated in this repository:
		i.e.: ~/git-clones/ChIP-Seq-Analysis/init
	4- Type "make"

If you have many processors avaible, you can use the "-j" option when calling make:
	make -j4

Dependencies:
	* Rscript (http://stat.ethz.ch/R-manual/R-patched/library/utils/html/Rscript.html)
	* MACS (http://liulab.dfci.harvard.edu/MACS/index.html)
	* ChIPpeakAnno (http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html)

Note: All the programs must be installed before starting the pipeline. Your PATH environment variable should contain the path to every dependency (except for R packages).