Course at EMBL-EBI

Introduction to RNA-seq and functional interpretation

This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. The content is intended to provide a broad overview of the subject area, and to introduce participants to simple data analysis using  the command line and APIs. It will also highlight key resources, approaches and methodologies to begin the biological interpretation and analysis of transcriptomics data. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets - there will be no opportunity to  analyse personal data.

Who is this course for?

This course is aimed at life science researchers wanting to learn more about processing RNA-Seq data and later downstream analysis. It will help those wanting a basic introduction to handling RNA-Seq data, guiding them through several common approaches that can be applied to their own datasets. It features taught and practical sessions that cover how to interpret gene expression data and learn more about the biological significance of certain results.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 18 operating system and the R statistical packages. We recommend these free tutorials:

Regardless of your current knowledge we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area.

What will I learn?

Learning outcomes

After this course you should be able to:

  • Describe a variety of applications and workflow approaches for NGS technologies

  • Use a range of bioinformatics software and tools to undertake basic analysis of RNA-Seq data
Evaluate the advantages and limitations of NGS analyses
  • Interpret and annotate data with functional information using public resources
Course content

During this course you will learn about:

  • RNA-Seq file formats and basics of experiemental design
  • RNA-Seq bioinformatics workflow steps following sequence generation

  • Methods for transcriptomics; QC, mapping, visualisation tools

  • Data resources to assist in the functional analysis and interpretation of transcriptomic data
  • Introduction to single-cell transcriptomics
  • Data resources covered:


Tom Hancocks
Malwina Prater
University of Cambridge, UK
Suhaib Mohammed
Silvie Fexova
Pablo Moreno
Kostas Billis
Leanne Haggerty
Jamie Allen
Denye Ogeh
Simon Andrews
Babraham Institute, UK
Liis Kolberg
University of Tartu, Estonia
Denise Carvalho-Silva
Thawfeek Mohamed Varusai
Asier Gonzalez
Irene Papatheodorou
Anton Petrov
Blake Sweeney


Day 1: Tuesday 21 January 2020
12:00-13:00 Arrival, registration, lunch  
13:00-14:00 Welcome, introductions and networking Tom Hancocks
14:00-15:30 Experimental design for RNA-Seq Malwina Prater
15:30-16:00 Break  
16:00-17:00 RNA-Seq file formats Suhaib Mohammed
17:00-18:00 Data reproducibility: standards and ontologies Silvie Fexova
18:00 End of day  
19:00 Evening meal Hinxton Hall Restaurant
20:30 Shuttle to Holiday Inn, Duxford  
Day 2 – Wednesday 22 January 2020
08:30 Shuttle to campus  
08:45 Arrival  
09:00-10:30 Annotating the genome with RNA-Seq data Leanne Haggerty & Kostas Billis
10:30-11:00 Break  
11:00-12:30 Introduction to RNA-Seq Simon Andrews
12:30-13:30 Lunch  
13:30-16:00 RNA-Seq practical Simon Andrews
16:00-16:30 Break  
16:30-18:30 Exploring gene expression data with Expression Atlas Silvie Fexova
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
20:30 Shuttle to Holiday Inn, Duxford  
Day 3 – Thursday 23 January 2020
08:30 Shuttle to campus  
08:45 Arrival  
09:00-11:00 Next steps in gene prioritisation Liis Kolberg
11:00-11:30 Break  
11:30-12:30 Next steps in gene prioritisation Liis Kolberg
12:30-13:30 Lunch  
13:30-15:30 Open Targets Platform: integrating human data for drug discovery Denise Carvalho-Silva & Asier Gonzalez
15:30-16:00 Break  
16:00-17:00 Towards single-cell RNA sequencing Irene Papatheodorou
17:70-18:30 Challenges in single-cell sequencing analysis Wendi Bacon
18:30 End of day  
18:45 Evening meal Red Lion Pub, Hinxton
21:00 Shuttle to Holiday Inn, Duxford  
Day 4 – Friday 24 January 2020
08:15 Checkout of accommodation  
08:30 Shuttle to campus  
08:45 Arrival  
09:00-10:00 Exploring biological pathways Thawfeek Varusai
10:00-11:00 Galaxy workflows for non-coding RNA Anton Petrov & Blake Sweeney
11:00-11:30 Break  
11:30-12:30 Galaxy workflows for non-coding RNA Anton Petrov & Blake Sweeney
12:30-12:45 Course wrap-up and feedback  
12:45-13:30 Lunch  
13:30 End of course  
13:45 Shuttle to Station Road, Cambridge  

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  1. Complete the online application form
  2. Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Marina Pujol (  by 12:00 GMT on Friday 4 October, 2019.

Incomplete applications will not be considered.

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21 - 24 January 2020
European Bioinformatics Institute United Kingdom
Marina Pujol

  • Tom Hancocks
  • Irene Papatheodorou

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