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|  NAME  |
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Differential Expression Analysis Pipeline on RNA-Seq data


Description
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This pipeline has been founded by IBISA-APLIBIO(http://www.renabi.fr/platforms/aplibio/), 
and has been built by (1)Yufei Luo, (2)Marie-Agnès Dillies, (1)Matthias Zytnicki and (1)Delphine Steinbach. 
(1): Bioinformatics plateform URGI, INRA URGI Versailles, France
(2): Plate-forme Transcriptome et Epigenome, Génopole, Institut Pasteur, France


This pipeline performs differential expression analysis on two different conditions with arbitrary number of replicates.

One reference genome (fasta format), one annotation (gtf format) and several RNA-seq samples are required.
Step 0: Upload RNA-seq samples.
Step 1: Clean the annotation file.
Step 2: Clean the RNA-seq files.
Step 3: Map the RNA-seq samples to the genome reference, using Tophat.
Step 4: Convert the bam files (given by Tophat) to sam files.
Step 5: Count the reads per annotation using S-MART (CompareOverlapping).
Step 6: Build the input files for DESeq.
Step 7: Differential expression analysis using DESeq, and output graphical results.

More information about using this pipeline, please see: http://urgi.versailles.inra.fr/galaxy/u/yluo/p/differential-expression-pipeline-documentation


Instructions
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Environment Installation:
0). First, download and install S-MART (eg from Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart).
1). Download and put the pipeline scripts directory under the S-MART directory
    (ex. mv DiffExpAnal /home/user/galaxy-dist/tools/s_mart/SMART/.).

Supplementary Softwares:
 * R, under the GNU General Public License (at least 2.14.1 version).
 * Python, under the Python License, compatible with the GNU General Public License (better 2.7)
 * S-MART (http://urgi.versailles.inra.fr/Tools/S-Mart), a toolbox which handles mapped RNA-Seq and ChIP-Seq data. 
 * DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html), an R package to analyse
   count data from high-throughput sequencing assays such as RNA-Seq and test
   for differential expression. The package is available via Bioconductor (http://www.bioconductor.org/)
   and can be conveniently installed as follows: 
     Start an R session and type:
     source("http://www.bioconductor.org/biocLite.R")
     biocLite("DESeq")
 * Biobase(http://www.bioconductor.org/packages/2.12/bioc/html/Biobase.html), an
   Bioconductor package and can be installed as follows:
     source("http://bioconductor.org/biocLite.R")
     biocLite("Biobase")


Copyright
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Copyright INRA-URGI 20012-2013


Authors
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Yufei Luo
Marie-Agnès Dillies
Matthias Zytnicki
Delphine Steinbach


Contact
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urgi-support@versailles.inra.fr


License
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This library is distributed under the terms of the CeCILL license 
(http://www.cecill.info/index.en.html).
See the LICENSE.txt file.


Acknowledgements
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Yufei Luo was supported by the Plant Breeding and Genetics research division of
the INRA, and by the Groupement d'intérêt scientifique IBISA.