IMPORTANT DATES for this Training course:

  • Deadline for applications: 30 June 2017
  • Course date: 18-20 July 2017

VENUE: Computer Room (aula Calcolo) Department of Biosciences, University of Milan (Via Celoria 26, Milan, Italy)

FEE: The course does not include a fee but the participants are expected to pay their own travel, meals and hotel costs (if any).

A maximum of 30 candidates will be accepted in the course. Selection will start on July 1st based on the candidates’ profile. Priority will be given to PhD students of the University of Milan and to candidates coming from abroad.



  • Giulio Pavesi (Dept. of Biosciences, University of Milano)
  • Federico Zambelli (Dept. of Biosciences, University of Milano and ELIXIR-IIB Technical Coordinator)
  • Matteo Chiara (Dept. of Biosciences, University of Milano)
  • Loredana Le Pera (ELIXIR-IIB Training Team)
  • Allegra Via (ELIXIR-IIB Training Coordinator, CNR, Italy)

Course Description

The course will provide students with theoretical and practical knowledge on how to perform bioinformatic analyses of RNA-Seq data, mainly aimed at the identification of genes differentially expressed across different conditions.

Target audience

PhD Students or young researchers in molecular biology and/or genetics with little or no background in bioinformatics.

Learning outcomes

After this course participants should be able to:

  • understand the theoretical principles of the analysis of RNA-Seq data
  • plan and execute the main steps of a bioinformatic RNA-Seq data analysis
  • use statistical approaches for the identification of differentially expressed genes
  • understand the results obtained

Course prerequisites

Basic background knowledge on genetics, molecular biology and transcriptomics.

Application Form


Tuesday - 18 July 2017

14:00 - 14:30 Opening and Welcome. Participants’ self-presentation
14:30 - 15:00 Lecture Giulio Pavesi Introduction to NGS and RNA-Seq
15:00 - 16:00 Lecture Matteo Chiara Theoretical principles in the analysis of RNA-Seq data.
16:00 - 16:30 Coffee break
16:30 - 17:30 Lecture Federico Zambelli Introduction to the Galaxy Platform

Wednesday - 19 July 2017

09:30 - 11:00 Practical Fabrizio Ferré Quality control, read mapping
11:00 - 11:30 Coffee break
11:30 - 13:00 Practical Fabrizio Ferré Read mapping and estimation of transcript levels
13:00 - 14:00 Lunch break
14:00 - 16:00 Practical Fabrizio Ferré Identification of differentially expressed genes
16:00 - 16:30 Coffe break
16:30 - 18:00 Practical Fabrizio Ferré Functional characterization of differentially expressed genes

Thursday - 20 July 2017

09:30 - 11:00 Lecture Giulio Pavesi Guidelines and strategies for post-processing of the results
11:00 - 12:00 Wrap-up and feedback

ELIXIR-IIB member institutions

  • CNR (ELIXIR-IIB coordinator)
  • CRS4
  • Fondazione Edmund Mach, Trento
  • INFN
  • GARR
  • Sapienza Università di Roma
  • Università di Bari
  • Università di Bologna
  • Università di Firenze
  • Università di Milano
  • Università di Milano Bicocca
  • Università di Padova
  • Università di Parma
  • Università di Roma "Tor Vergata"
  • Università di Salerno
  • Università della Tuscia