Forty-one trainees sponsored by COST FA 1106 for a total budget of 46k€  have already attended to one of the three Training School organized by leading scientist in their fields.

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Training School RNA-Seq data analysisToulouse, March 6-8th, 2013

The RNA-Seq training school was held at ENSA Toulouse (France)


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.


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



-          Mohamed Zouine, GBF, INP/INRA Toulouse



-        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


Pierre-François Bert

INRA Univ Bordeaux

Efstathios Roumeliotis

Aristotle University of Thessaloniki

Maria Manioudaki

Mediterranean Agronomic Institute of Chania


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)