Training School RNA-Seq data analysisToulouse, March 6-8th, 2013
The RNA-Seq training school was held at ENSA Toulouse (France)
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QualityFruit in partnership with the bioinformatic plateforme GenoToule-Bioinfo offered a training courses for bio-informaticians and biologists aiming at familiarizing them with the analysis of sequences produced by second-generation sequencers and application on RNA-Seq data analysis.
This training session was designed to help you deal with sequences from the SGS (Second Generation Sequencing) particularly Illumina platforms (GAIIx, HiSeq). You will discover the new sequence file formats, learn about the usual biases of this data type and run different kind of analysis such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of the genes and transcripts and statistical analysis to identify differentially expressed genes.
Program:
This training focused on practice. It was composed of three working days and four modules with a large variety of exercises.
Day 1: Wednesday, March 6th
10h - 12h: Registration
12h - 14h: Lunch
14h-14h30: Welcome talk by the Chair
14h30 – 16h: How to use the UNIX command line environment
16h-16h20: Coffee break at
16h20 – 18h30: How to use the UNIX command line environment (Continue)
18h30-20h30: French Wine tasting and local food.
Day 2: Thursday, March 7th
9h -10h30: RNA-seq data analysis: Sequence quality (theory + exercices)
1030h-10h50: Coffee break
10h50 -12h30: Spliced read mapping and visualisation (theory + exercices)
12h30 - 13h30: Lunch
13h30 - 15h30: Expression measurements (theory + exercices)
15h30 - 15h50: Coffee break at 16h-16h20
15h50 - 18h: mRNA calling (theory + exercices)
19h30-22h30: Social Diner at a restaurant
Day 3: Friday, March 8th
9h -10h30: Introduction to R environment
10h30 – 10h45: Coffee break
10h45 – 12h: RNA-seq data normalization and Identification of DE genes
12h - 13h30: Lunch
13h30 - 16h30: Data mining
16h30- 17h: Appraisal and departure
Organiser:
- Mohamed Zouine, GBF, INP/INRA Toulouse
Teachers:
- Christophe Klopp , Genotoul-Bioinfo, INRA, Toulouse
- Celine Noirot, Genotoul-Bioinfo, INRA, Toulouse
- Delphine Labourdette, Genotoul-Bioinfo, INRA, Toulouse
- Elie Maza , GBF, INP/INRA Toulouse
- Matthieux Lauvernier, GBF, INP/INRA Toulouse
- Antonio Granell-Richard, CSIC, Valencia.
- Maria Luisa Chiusano, University "Federico II" of Naples
- Mohamed Zouine, GBF, INP/INRA Toulouse
Participants :
Katharina Lang |
University of Natural Resources and Life Sciences Vienna |
Chrystalla Antoniou |
Cyprus University of Technology |
Jens Dudenhöffer |
Julius Kühn-Institut, Institute for Grapevine Breeding |
Miguel Ramos |
Instituto Superior de Agronomia |
Sonia Osorio |
University of Malaga |
Rafael Torres |
Centro Nacional de Biotecnología |
Martine Lemaire-Chamley |
INRA-Bordeaux |
Pierre-François Bert |
INRA Univ Bordeaux |
Efstathios Roumeliotis |
Aristotle University of Thessaloniki |
Maria Manioudaki |
Mediterranean Agronomic Institute of Chania |
Itay MAOZ |
Agricultural Research Organization - the Volcani Center |
Stefania Savoi |
Udine University |
Marco Pietrella |
ENEA, Rome |
Hamed Bostan |
Dept. of Soil, Plant, Environmental, Naples |
Mélanie Massonnet |
University of Verona |
Marianna Fasoli |
University of Verona |
Massimiliano Corso |
University of Padova (Italy) |
Olfa Zarrouk |
Instituto de Tecnologia Química e Biológica |
Gurgu Leontina |
University of Galati, Romania |
For any question, please contact Mohamed Zouine (mohamed.zouine @ ensat.fr).