# HG changeset patch
# User yufei-luo
# Date 1358945864 18000
# Node ID 839800dfba59ed62c9b054113a4d492fe71c4780
# Parent  59cc55f611f6e30a01061108f991205f265d83ed
Uploaded

diff -r 59cc55f611f6 -r 839800dfba59 README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Wed Jan 23 07:57:44 2013 -0500
@@ -0,0 +1,82 @@
+----------
+|  NAME  |
+----------
+Differential Expression Analysis Pipeline on RNA-Seq data
+
+
+Description
+-----------
+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
+------------
+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
+---------
+Copyright INRA-URGI 20012-2013
+
+
+Authors
+-------
+Yufei Luo
+Marie-Agnes Dillies
+Matthias Zytnicki
+Delphine Steinbach
+
+
+Contact
+-------
+urgi-support@versailles.inra.fr
+
+
+License
+-------
+This library is distributed under the terms of the CeCILL license 
+(http://www.cecill.info/index.en.html).
+See the LICENSE.txt file.
+
+
+Acknowledgements
+----------------
+Yufei Luo was supported by the Plant Breeding and Genetics research division of
+the INRA, and by the Groupement d'intérêt scientifique IBISA.