annotate dexseq-hts_1.0/README @ 11:cec4b4fb30be draft default tip

DEXSeq version 1.6 added

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A Galaxy wrapper for DEXSeq version 1.6.0
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DEXSeq is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. 
DEXSeq: http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html

Requirements:
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    Python, HTSeq package :- Preprocessing of sequencing reads and GFF files
    R, Bio-conductor package :- Required for DEXSeq 
    SAMTOOLS :- Sequencing read processing 

Contents:
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./bin 
    Contains a config file for running DEXSeq in different settings, setup_dexseq-hts.sh
    will help to create the config file according to your local work station. 

./setup_dexseq-hts.sh
    Setup script, which helps to set the right path to the config file present in the bin
    folder. 
    
./README 
    Basic information about the wrapper 

./galaxy 
    Galaxy tool configuration file can be found here. 

./src
    All relevant scripts for DEXSeq execution, Please follow the shell script to 
    understand the details.

Licenses:
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    If DEXSeq is used to obtain results for scientific publications it should be cited as [1].

    This wrapper program is free software; you can redistribute it and/or modify it under the 
    terms of the GNU General Public License as published by the Free Software Foundation; either 
    version 3 of the License, or (at your option) any later version.

    Copyright(C) 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.

References
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    [1] Simon Anders and Alejandro Reyes and Wolfgang Huber (2012): Detecting differential usage of exons from RNA-seq data. 

Contact:
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    support [at] oqtans.org