Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
changeset 7:839800dfba59 draft
Uploaded
author | yufei-luo |
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date | Wed, 23 Jan 2013 07:57:44 -0500 |
parents | 59cc55f611f6 |
children | 6f010c2163c1 |
files | README.txt |
diffstat | 1 files changed, 82 insertions(+), 0 deletions(-) [+] |
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--- /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.