Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
changeset 8:6f010c2163c1 draft
Deleted selected files
| author | yufei-luo |
|---|---|
| date | Wed, 23 Jan 2013 07:58:17 -0500 |
| parents | 839800dfba59 |
| children | a03838a6eb54 |
| files | DiffExpAnal/README.txt README.txt |
| diffstat | 2 files changed, 0 insertions(+), 164 deletions(-) [+] |
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--- a/DiffExpAnal/README.txt Wed Jan 23 07:57:44 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ ----------- -| 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-Agnès 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.
--- a/README.txt Wed Jan 23 07:57:44 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ ----------- -| 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.