comparison DiffExpAnal/README.txt @ 9:a03838a6eb54 draft

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author yufei-luo
date Wed, 23 Jan 2013 07:58:38 -0500
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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
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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.