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Updated DESeq version 1.12
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:09:28 -0400
parents 8ab01cc29c4b
children
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8:2b3bb3348076 9:e27b4f7811c2
1 --------------------------------------------------- 1 ----------------------------------------------------
2 DESeq-hts: A Galaxy wrapper for DESeq version 1.6.1 2 DESeq: A Galaxy wrapper for DESeq version 1.12.1
3 --------------------------------------------------- 3 ----------------------------------------------------
4 4
5 Description: 5 Description:
6 ------------
6 DESeq can be used as a web service embedded in a Galaxy instance. 7 DESeq can be used as a web service embedded in a Galaxy instance.
7 We call it as DESeq-hts. 8 We call it as DESeq-hts.
8 9
9 Requirements: 10 Requirements:
11 -------------
10 MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files 12 MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
11 R, Bio-conductor package :- Required for DESEQ 13 R, Bio-conductor package :- Required for DESeq
12 SCIPY, NUMPY :- for python 14 SCIPY, NUMPY :- for python
13 SAMTOOLS :- Read processing 15 SAMTOOLS :- Sequencing read processing
14 16
15 Contents: 17 Contents:
16 [src] 18 ---------
19 ./src
17 All relevant scripts for DESeq-hts are located in the subdirectory 20 All relevant scripts for DESeq-hts are located in the subdirectory
18 src. src/deseq.sh is the main script to start DESeq-hts. The 21 src. src/deseq-hts.sh is the main script to start DESeq-hts. The
19 preprocessing of BAM and GFF file start before the R DESEQ script. 22 preprocessing of BAM and GFF file start before the R DESeq script.
20 Please follow the shell script to understand the details. 23 Please follow the shell script to understand the details.
21 24
22 [galaxy] 25 ./galaxy
23 Galaxy tool configuration file can be found galaxy folder. Please 26 Galaxy tool configuration file can be found galaxy folder. Please
24 make necessary editing for .xml file and remaining .sh files and 27 make necessary editing for .xml file and remaining .sh files and
25 perform few tests. 28 perform few tests.
26 29
27 [setup_deseq-hts.sh] 30 ./setup_deseq-hts.sh
28 Setup script for DESeq-hts. 31 Setup script for DESeq-hts.
29 32
30 [mex] 33 ./mex
31 matlab executable files. 34 matlab executable files.
32 35
33 [bin] 36 ./bin
34 Contains deseq_config.sh file which is used for the configuration of 37 Contains deseq_config.sh file which is used for the configuration of
35 DESeq-hts. According to your platform, the default file will be changed. 38 DESeq-hts. According to your platform, the default file will be changed.
36 39
37 [test_data] 40 ./test_data
38 This subsirectory contains all data for running a functional test in 41 This sub-directory contains all data for running a functional test in
39 Galaxy framework. You may need to move these test files into the test-data 42 Galaxy framework. You may need to move these test files into the test-data
40 directory. 43 directory.
41 44
42 [tools] 45 ./tools
43 A python based GFF parsing program. Also contains small utils programs. 46 A python based GFF parsing program. Also contains small utils programs.
44 47
45 Getting started: 48 Getting started:
49 ----------------
46 Check for all requirements first, then 50 Check for all requirements first, then
47 51
48 a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. 52 a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.
49 53
50 b) Inside the mex folder execute the make file to create platform dependent .mex files 54 b) Inside the mex folder execute the make file to create platform dependent .mex files
55 make all for octave and matlab 59 make all for octave and matlab
56 60
57 c) Edit the Galaxy tool configuration file to adjust the path if necessary. 61 c) Edit the Galaxy tool configuration file to adjust the path if necessary.
58 62
59 Licenses: 63 Licenses:
64 ---------
60 If **DESeq** is used to obtain results for scientific publications it should be cited as [1]. 65 If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
61 66
62 This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it 67 This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it
63 under the terms of the GNU General Public License as published by the Free Software Foundation; 68 under the terms of the GNU General Public License as published by the Free Software Foundation;
64 either version 3 of the License, or (at your option) any later version. 69 either version 3 of the License, or (at your option) any later version.
65 70
66 Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan 71 Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
67 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and 72 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and
68 2012 cBio Memorial Sloan Kettering Cancer Center, New York City, USA. 73 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
69 74
70 References: 75 References:
76 -----------
71 [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`. 77 [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.
72 78
79 Contributions:
80 --------------
81 15 Aug. 2013
82 Philippe Moncuquet
83 Bioinformatics Analyst, Bioinformatics Core, CSIRO Mathematics, Informatics and Statistics
84
85 Extended the DESeq result.
86
73 Contact: 87 Contact:
74 vipin@cbio.mskcc.org 88 --------
89 support [at] oqtans.org
75 90