Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
comparison README.txt @ 7:839800dfba59 draft
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| author | yufei-luo |
|---|---|
| date | Wed, 23 Jan 2013 07:57:44 -0500 |
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| 6:59cc55f611f6 | 7:839800dfba59 |
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| 1 ---------- | |
| 2 | NAME | | |
| 3 ---------- | |
| 4 Differential Expression Analysis Pipeline on RNA-Seq data | |
| 5 | |
| 6 | |
| 7 Description | |
| 8 ----------- | |
| 9 This pipeline has been founded by IBISA-APLIBIO(http://www.renabi.fr/platforms/aplibio/), | |
| 10 and has been built by (1)Yufei Luo, (2)Marie-Agnès Dillies, (1)Matthias Zytnicki and (1)Delphine Steinbach. | |
| 11 (1): Bioinformatics plateform URGI, INRA URGI Versailles, France | |
| 12 (2): Plate-forme Transcriptome et Epigenome, Génopole, Institut Pasteur, France | |
| 13 | |
| 14 | |
| 15 This pipeline performs differential expression analysis on two different conditions with arbitrary number of replicates. | |
| 16 | |
| 17 One reference genome (fasta format), one annotation (gtf format) and several RNA-seq samples are required. | |
| 18 Step 0: Upload RNA-seq samples. | |
| 19 Step 1: Clean the annotation file. | |
| 20 Step 2: Clean the RNA-seq files. | |
| 21 Step 3: Map the RNA-seq samples to the genome reference, using Tophat. | |
| 22 Step 4: Convert the bam files (given by Tophat) to sam files. | |
| 23 Step 5: Count the reads per annotation using S-MART (CompareOverlapping). | |
| 24 Step 6: Build the input files for DESeq. | |
| 25 Step 7: Differential expression analysis using DESeq, and output graphical results. | |
| 26 | |
| 27 More information about using this pipeline, please see: http://urgi.versailles.inra.fr/galaxy/u/yluo/p/differential-expression-pipeline-documentation | |
| 28 | |
| 29 | |
| 30 Instructions | |
| 31 ------------ | |
| 32 Environment Installation: | |
| 33 0). First, download and install S-MART (eg from Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart). | |
| 34 1). Download and put the pipeline scripts directory under the S-MART directory | |
| 35 (ex. mv DiffExpAnal /home/user/galaxy-dist/tools/s_mart/SMART/.). | |
| 36 | |
| 37 Supplementary Softwares: | |
| 38 * R, under the GNU General Public License (at least 2.14.1 version). | |
| 39 * Python, under the Python License, compatible with the GNU General Public License (better 2.7) | |
| 40 * S-MART (http://urgi.versailles.inra.fr/Tools/S-Mart), a toolbox which handles mapped RNA-Seq and ChIP-Seq data. | |
| 41 * DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html), an R package to analyse | |
| 42 count data from high-throughput sequencing assays such as RNA-Seq and test | |
| 43 for differential expression. The package is available via Bioconductor (http://www.bioconductor.org/) | |
| 44 and can be conveniently installed as follows: | |
| 45 Start an R session and type: | |
| 46 source("http://www.bioconductor.org/biocLite.R") | |
| 47 biocLite("DESeq") | |
| 48 * Biobase(http://www.bioconductor.org/packages/2.12/bioc/html/Biobase.html), an | |
| 49 Bioconductor package and can be installed as follows: | |
| 50 source("http://bioconductor.org/biocLite.R") | |
| 51 biocLite("Biobase") | |
| 52 | |
| 53 | |
| 54 Copyright | |
| 55 --------- | |
| 56 Copyright INRA-URGI 20012-2013 | |
| 57 | |
| 58 | |
| 59 Authors | |
| 60 ------- | |
| 61 Yufei Luo | |
| 62 Marie-Agnes Dillies | |
| 63 Matthias Zytnicki | |
| 64 Delphine Steinbach | |
| 65 | |
| 66 | |
| 67 Contact | |
| 68 ------- | |
| 69 urgi-support@versailles.inra.fr | |
| 70 | |
| 71 | |
| 72 License | |
| 73 ------- | |
| 74 This library is distributed under the terms of the CeCILL license | |
| 75 (http://www.cecill.info/index.en.html). | |
| 76 See the LICENSE.txt file. | |
| 77 | |
| 78 | |
| 79 Acknowledgements | |
| 80 ---------------- | |
| 81 Yufei Luo was supported by the Plant Breeding and Genetics research division of | |
| 82 the INRA, and by the Groupement d'intérêt scientifique IBISA. |