Key details

Course website: Introduction to RNA-seq and functional interpretation

Course dates: 22 – 26 February 2027

Location: Virtual, UK time zone

Provider: EMBL-EBI Training

Applications close: 22 November 2026

Course fee: £250.00 (academia) / £350.00 (industry). Financial support is available.

Overview

In this course delivered by the training department of EMBL's European Bioinformatics Institute (EMBL-EBI), we will guide you through the core technology, data analysis approaches, tools, and resources used in RNA sequencing (RNA-seq) and transcriptomics. Our goal is to support you as you build a shared understanding of the field, whether your background is in biology, computer science, or data analysis. We will introduce the fundamental concepts behind transcriptomic workflows and help you gain confidence with basic command‑line analysis.

Together, we'll explore key public data repositories and outline the main methodologies that can help you begin the biological interpretation of gene expression data. Throughout the course, a mix of learning through lectures, practical exercises, and open discussions will create an environment where you can engage with the material from your own disciplinary perspective.

All computational work will use small example data sets so that you can focus on learning the concepts and workflows. Please note that there will be no opportunity to analyse personal data during the course.

Virtual course

You will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.

Pre-recorded material may be provided before the course starts; participants will need to watch, read, or work through to gain the most out of the actual training event. In the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, so you will not require access to a powerful computer or install software on your own machine.

You will need to be available between the hours of 09:00 – 17:30 UK time each day of the course. Trainers will be available to assist, answer questions, and provide further explanations to you during these times.

Who is this course for?

This course is aimed at life science researchers, wet and/or dry lab, wanting to learn more about processing RNA-seq data and later downstream analysis. It will help you if you want a basic introduction to handling RNA-seq data. We'll guide you through several common approaches that can be applied to your own datasets. The course features taught and practical sessions that cover how to interpret gene expression data and learn more about the biological significance of certain results.

Some experience with R and the Linux-based command line is beneficial, but not essential. During the course, some of the practicals will make use of a Linux-based command line interface and R statistical packages. We recommend completing some basic tutorials on this topic in preparation for the upcoming course.

Course content

During this course, you will learn about:

• High-throughput sequencing technologies for RNA-Seq
• Basics of experimental design
• RNA-seq file formats
• RNA-seq bioinformatics workflow steps following sequence generation
• Methods for transcriptomics; QC, mapping, and visualisation tools
• Data resources to assist in the functional analysis and interpretation of transcriptomic data
• Introduction to long read analysis
• Fundamentals of pipeline implementation (with Nextflow) for bulk RNA-seq analysis
• Data resources covered: Expression Atlas and g:Profiler
• Sequencing repositories: ENA, GEO, SRA

After the course you should be able to:

• Describe a variety of applications and workflow approaches for NGS technologies
• Apply bioinformatics software and tools to undertake analysis of RNA-seq data
• Evaluate the advantages and limitations of NGS analyses
• Interpret and annotate data with functional information using public resources

Trainers

Simon Andrews, Babraham Institute

Vladimir Benes, EMBL Heidelberg

Sarah Inglesfield, Babraham Institute

Alexey Larionov, Cranfield University

Geraldine Van der Auwera, Seqera

Liora Vilmovsky, EMBL-EBI

Organisers

Simon Andrews, Babraham Institute

Lizzie Bridget Divala, EMBL-EBI

Toke Labiyi, EMBL-EBI

Alexey Larionov, Cranfield University