Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/release_note @ 0:acc2ca1a3ba4
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| author | siyuan |
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| date | Thu, 20 Feb 2014 00:44:58 -0500 |
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| -1:000000000000 | 0:acc2ca1a3ba4 |
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| 1 PRADA: Pipeline for RnAseq Data Analysis | |
| 2 | |
| 3 AUTHOR: Siyuan Zheng, Wandaliz-Torres Garcia, Rahul Vegesna | |
| 4 CONTACT: Siyuan Zheng (szheng2@mdanderson.org), Roel Verhaak (rverhaak@mdanderson.org) | |
| 5 COPY RIGHT: Verhaak Lab,Department of Bioinformatics and Computational Biology | |
| 6 The University of Texas MD Anderson Cancer Center | |
| 7 VERSION: 1.2 | |
| 8 DATE: 02/16/2014 | |
| 9 REQUIRE: Python v2.6 or v2.7; | |
| 10 Python Libs: pysam, Biopython | |
| 11 PLATFORM: Linux, tested with PBS, B-shell and TC-shell | |
| 12 | |
| 13 CITATION | |
| 14 PRADA: Pipeline for RNA sequencing Data Analysis | |
| 15 Bioinformatics. Coming soon. | |
| 16 | |
| 17 TOOLS INCLUDED: | |
| 18 prada-fusion genome-widely identify gene fusions | |
| 19 prada-preprocess preprocess paired end RNAseq data | |
| 20 prada-frame predict functional consequences of gene fusions | |
| 21 prada-homology calculate gene sequence similarity | |
| 22 prada-guess-ft supervised search of a gene fusion | |
| 23 prada-guess-if supervised search of intragenic fusions (normal splicing excluded) | |
| 24 | |
| 25 WHAT'S NEW | |
| 26 1. New configur allows more user customization to bwa alignment and PBS script. | |
| 27 2. Reorganized preprocess module for better control of BAM an FASTQ as input. | |
| 28 3. A test data set is added. |