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README
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TODO list
get rid of support for octave from counting
compute_sequence_read.py program should work with GTF/GFF file and multiple BAM files
python to talk with c++ counting script will be a good idea,
give rights to access count table from other programs too the interface. gff/bam or count table and the condition details
single dependency folder for tools
test-data set more comprehensive
----------------------------------------------------
DESeq-hts: A Galaxy wrapper for DESeq version 1.10.1
----------------------------------------------------
Description:
------------
DESeq can be used as a web service embedded in a Galaxy instance.
We call it as DESeq-hts.
Requirements:
-------------
MATLAB/OCTAVE and Python :- Preprocessing of sequencing reads and GFF files
R, Bio-conductor package :- Required for DESeq
SCIPY, NUMPY :- for python
SAMTOOLS :- Sequencing read processing
Contents:
---------
./src
All relevant scripts for DESeq-hts are located in the subdirectory
src. src/deseq-hts.sh is the main script to start DESeq-hts. The
preprocessing of BAM and GFF file start before the R DESeq script.
Please follow the shell script to understand the details.
./galaxy
Galaxy tool configuration file can be found galaxy folder. Please
make necessary editing for .xml file and remaining .sh files and
perform few tests.
./setup_deseq-hts.sh
Setup script for DESeq-hts.
./mex
matlab executable files.
./bin
Contains deseq_config.sh file which is used for the configuration of
DESeq-hts. According to your platform, the default file will be changed.
./test_data
This sub-directory contains all data for running a functional test in
Galaxy framework. You may need to move these test files into the test-data
directory.
./tools
A python based GFF parsing program. Also contains small utils programs.
Getting started:
----------------
Check for all requirements first, then
a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts.
b) Inside the mex folder execute the make file to create platform dependent .mex files
cd mex/Makefile
make [interpreter]
make octave for octave
make matlab for matlab
make all for octave and matlab
c) Edit the Galaxy tool configuration file to adjust the path if necessary.
Licenses:
---------
If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
This wrapper program (DESeq-hts) is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free Software Foundation;
either version 3 of the License, or (at your option) any later version.
Written (W) 2009-2012 Jonas Behr, Regina Bohnert, Andre Kahles, Gunnar Raetsch, Vipin T. Sreedharan
Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany and
2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
References:
-----------
[1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.
Contributions:
--------------
15 Aug. 2013
Philippe Moncuquet
Bioinformatics Analyst, Bioinformatics Core, CSIRO Mathematics, Informatics and Statistics
Extended the DESeq result.
Contact:
--------
vipin [at] cbio.mskcc.org