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1 PRADA: Pipeline for RnAseq Data Analysis
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2
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3 AUTHOR: Siyuan Zheng, Wandaliz-Torres Garcia, Rahul Vegesna
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4 CONTACT: Siyuan Zheng (szheng2@mdanderson.org), Roel Verhaak (rverhaak@mdanderson.org)
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5 COPY RIGHT: Verhaak Lab,Department of Bioinformatics and Computational Biology
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6 The University of Texas MD Anderson Cancer Center
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7 VERSION: 1.2
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8 DATE: 02/16/2014
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9 REQUIRE: Python v2.6 or v2.7;
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10 Python Libs: pysam, Biopython
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11 PLATFORM: Linux, tested with PBS, B-shell and TC-shell
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12
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13 CITATION
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14 PRADA: Pipeline for RNA sequencing Data Analysis
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15 Bioinformatics. Coming soon.
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16
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17 TOOLS INCLUDED:
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18 prada-fusion genome-widely identify gene fusions
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19 prada-preprocess preprocess paired end RNAseq data
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20 prada-frame predict functional consequences of gene fusions
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21 prada-homology calculate gene sequence similarity
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22 prada-guess-ft supervised search of a gene fusion
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23 prada-guess-if supervised search of intragenic fusions (normal splicing excluded)
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24
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25 WHAT'S NEW
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26 1. New configur allows more user customization to bwa alignment and PBS script.
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27 2. Reorganized preprocess module for better control of BAM an FASTQ as input.
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28 3. A test data set is added.
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