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