Introduction to RNA-Seq and Functional Interpretation


 Tuesday 26 Friday 29 March 2019


European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday October 01 2018

Application deadline: 

Friday December 14 2018


Open application with selection


Johanna Langrish

Registration fee: 



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.


This course is aimed at life science researchers needing to learn more about the basic processing of raw RNA-Seq data and downstream analysis. It will help those wanting to learn how to interpret gene expression data and explore results of biological significance from processed data.

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.

Syllabus, tools and resources

During this course you will learn about:

  • NGS platforms and NGS data files and formats

  • RNA-Seq bioinformatics workflow steps following sequence generation

  • NGS for transcriptomics; QC, mapping, visualisation tools

  • Data resources to assist in the functional analysis and interpretation of biological data
  • Data resources covered:
    • ArrayExpress and Expression Atlas
    • European Nucleotide Archive
    • Reactome
    • Open Targets


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



Day 1 – Tuesday 26 March 2018
12:00 - 13:00 Arrival, registration and lunch  
13:00 - 14:00 Introductions, expectations and EMBL-EBI overview Tom Hancocks
14:00 - 15:30 Introduction to NGS and RNA-Seq Tom Hancocks
15:30 - 16:00 Break  
16:00 - 17:30 RNA-Seq file formats practical To be confirmed
17:30 - 18:30 Data reproducibility: standards and ontologies Laura Huerta Martinez
18:30 End of day  
18:45 Evening meal Hinxton Hall
20:15 Coach to Holiday Inn, Impington  
Day 2 – Wednesday 27 March 2018
08:00 Coach to Campus  
08:45 Arrival  
09:00 - 10:30 Annotating the genome with RNA-Seq data Ensembl Genebuild
10:30 - 11:00 Break
11:00 - 12:30 Introduction to RNA-Sequencing Babraham Bioinformatics
12:30 - 13:30 Lunch
13:30 - 16:00 RNA-Sequencing Babraham Bioinformatics
16:00 - 16:30 Break  
16:30 - 17:30 Transcript and isoform quantification To be confirmed
17:30 - 18:30 Access to RNA-Seq analysis results with the RNASeq-er API To be confirmed
18:45 Evening meal Hinxton Hall
20:15 Coach to Holiday Inn, Impington  
Day 3 – Thursday 28 March 2018
08:00 Coach to Campus  
08:45 Arrival  
09:00 - 11:00 Exploring gene expression data with Expression Atlas Expression Atlas Team
11:00 - 11:30 Break
11:30 - 13:30 Next steps in gene prioritisation To be confirmed
13:00 - 14:00 Lunch
14:00 - 16:00 Exploring biological pathways Reactome Team
16:00 - 16:30 Break  
16:30 - 18:30 Integreating biological data Open Targets Team
18:45 Evening meal Hinxton Hall
20:15 Coach to Holiday Inn, Impington  
Day 4 – Friday 29 March 2018
08:00 Checkout of Holiday Inn, Coach to Campus  
08:45 Arrival  
09:00 - 10:00 RNA data resources RNA-Central Team
10:00 - 11:00 Nucleotide sequence repository ENA Team
11:00 - 11:30 Break  
12:30 - 12:45 Feedback and course wrap-up Tom Hancocks
12:45 - 13:30 Lunch  
13:30 Coach to Cambridge Station