IBISA-RNASeq
IBISA-RnaSeq is a project funded by GIS IBISA, that involves Aplibio-RENABI bioinformatics platform in the aim of developping software tools for NGS analysis. URGI partner is the developper team of this project. The collection of needs is made in collaboration of Aplibio network. The environment chosen to host these new tools and workflows, is Galaxy.
Duration: 01/10/2011 to 30/04/2013
Coordinator: Delphine Steinbach, Matthias Zytnicki
Partners:
Aplibio bioinformatics network coordinated by Ivan Moszer, Institut Pasteur
for this project are involved in the working group :
- Bioinformatics Platform/facility: INRA URGI : YuFei Luo (Galaxy developper), Matthias Zytnicki (SMART author, developer, scientific management), Delphine Steinbach (project coordination, member of Aplibio steering commitee)
- Bioinformatics Platform at Institut Curie represented by :
- Bioinformatics, Genomics platforms at Institut Pasteur represented by Ivan Moszer
- Bioinformatics Platform eBio at Orsay : represented by Claire Toffano and Daniel Gautheret
Developments are made by YuFei Luo at URGI, 18 months
Results
- a first workflow for eBio platform project was developped and presented to partners in may 2012. This workflow was transfered at eBio and is currently in improvement for final release and documentation writting (Paper in prep. Claire Toffano & al.) Training session organized on Ebio site, planned for autumn.
- a second workflow asked by URGI, eBio, Institut Pasteur, Institut Curie is currently in development since march 2012 to analyse RNA-Seq sequences for differential analysis. A first version of the workflow based on DESeq package was shown in may 2012. A new improved version is currently in development.
A poster will be presented to Galaxy conference in Chicago in July 2012. (YuFei Luo &al.)
A training session based on Galaxy tools for RNASeq is planned the 11 of July, to be applied for Maize needs.
For interest concerning the tools and the workflow, please, contact Delphine Steinbach and Matthias Zytnicki at URGI.