PRADA: Pipeline for RnAseq Data Analysis

AUTHOR: 		Siyuan Zheng, Wandaliz-Torres Garcia, Rahul Vegesna
CONTACT: 		Siyuan Zheng (szheng2@mdanderson.org), Roel Verhaak (rverhaak@mdanderson.org)
COPY RIGHT: 	Verhaak Lab,Department of Bioinformatics and Computational Biology
				The University of Texas MD Anderson Cancer Center
VERSION: 		1.2
DATE:			02/16/2014
REQUIRE:		Python v2.6 or v2.7; 
Python Libs:	pysam, Biopython
PLATFORM:		Linux, tested with PBS, B-shell and TC-shell

CITATION
PRADA: Pipeline for RNA sequencing Data Analysis
Bioinformatics. Coming soon. 

TOOLS INCLUDED:
prada-fusion		genome-widely identify gene fusions 
prada-preprocess	preprocess paired end RNAseq data
prada-frame			predict functional consequences of gene fusions
prada-homology		calculate gene sequence similarity
prada-guess-ft		supervised search of a gene fusion
prada-guess-if		supervised search of intragenic fusions (normal splicing excluded)

WHAT'S NEW
1. New configur allows more user customization to bwa alignment and PBS script. 
2. Reorganized preprocess module for better control of BAM an FASTQ as input.
3. A test data set is added.