Virtual course
Introduction to RNA-seq and functional interpretation
2027
In this course, 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. There are many tutorials available online, here are some that may be of help:
What will I learn?
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
Learning outcomes
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
Programme
Time | Topic | Trainer |
Day one – Monday 22 February 2027 | ||
09:00 — 10:00 | Welcome and course introduction | Lizzie Divala |
10:00 – 11:00 | Course overview | Vladimir Benes |
11:00 — 11:10 | Coffee break | |
11:10 – 12:10 | Experimental design | Vladimir Benes |
12:10 – 13:10 | Lunch Break | |
13:10 – 14:10 | Introduction to sequencing | Vladimir Benes |
14:10 – 14:30 | Break | |
14:30 – 15:30 | Navigating sequencing data: format, quality, and repositories | Sarah Inglesfield |
15:30 – 15:40 | Break | |
15:40 – 17:30 | Sequencing repositories | Sarah Inglesfield |
17:30 | End of day | |
Day two – Tuesday 23 February 2027 | ||
09:00 – 10:30 | Introduction to RNA-seq | Simon Andrews |
10:30 – 11:00 | Break | |
11:00 – 13:00 | RNA-seq practical | Simon Andrews |
13:00 – 14:00 | Lunch Break | |
14:00 – 15:30 | RNA-seq practical | Simon Andrews |
15:30 – 16:00 | Break | |
16:00 – 17:30 | RNA-seq practical | Simon Andrews |
17:30 – 18:00 | Flash talks one | |
18:00 | End of day | |
Day three – Wednesday 24 February 2027 | ||
09:00 – 10:00 | Annotating the genome with RNA-seq data | TBC |
10:00 – 10:10 | Break | |
10:10 – 12:00 | Genome annotation practical | TBC |
12:00 – 13:00 | Lunch break | |
13:00 – 14:00 | Long-read RNA-seq analysis | Alexey Larionov |
14:00 – 14:20 | Break | |
14:20 – 17:00 | Long-read RNA-seq analysis | Alexey Larionov |
17:00 – 17:30 | Flash talks two | |
17:30 | End of day | |
Day four – Thursday 25 February 2027 | ||
09:00 – 10:20 | Next steps in gene prioritisation | TBC |
10:20 – 10:40 | Break | |
10:40 – 12:30 | Next steps in gene prioritisation | TBC |
12:30 – 13:30 | Lunch Break | |
13:30 – 14:30 | Data reproducibility: standards and ontologies – lecture and activity | TBC |
14:30 – 15:00 | Break | |
15:00 – 16:00 | Exploring gene expression data | Liora Vilmovsky |
16:00 – 17:00 | Flash talks three | |
17:00 | End of day | |
Day five – Friday 26 February 2027 | ||
09:00 – 10:30 | Pipeline implementation workshop | Geraldine Van der Auwera |
10:30 – 10:45 | Break | |
10:45 – 12:30 | Pipeline implementation workshop | Geraldine Van der Auwera |
12:30 – 13:30 | Lunch break | |
13:30 – 16:30 | Pipeline implementation workshop | Geraldine Van der Auwera |
16:30 – 17:00 | Course wrap-up | Lizzie Divala |
17:00 | End of day | |
Please read our support page before starting your application.
You will need to submit all documents during the application process by 23:59 UK time on 22 November 2026.
You will then be informed of the status of your application (successful, waiting list, or unsuccessful) by 4 December 2026.
If you have any questions regarding the application process, please contact your Event Organiser, Toke Labiyi.
Flash talks
If selected for this course, you will be asked to submit your flash talk upon registration. This should be a short presentation about your research work, providing you with an opportunity to share your research with the other attendees and provide a forum for discussion.
Registration fees
Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.
Your registration fee includes:
- access to the full five-day course programme
- access to a bespoke online course handbook
- secure community space on Slack
- virtual machine to work on that is accessed via the internet
- dedicated online support team
- certificate on completion of the course
Academia | £250.00 |
Industry* | £350.00 |
* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.
Financial assistance
- Financial assistance is available to a limited number of participants attending this course. For full details, please refer to our dedicated support page for information on available fee waivers, travel grants, and financial assistance.
Event terms and conditions
- By applying and registering for events hosted by EMBL-EBI Training, you are adhering to our terms and conditions. We recommend that you read through these before submitting your details.
Course materials
- The materials for the 2026 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2027 course.
The EMBL-EBI Training team is committed to making our events inclusive and accessible to all participants, whether attending onsite or virtually. Please read our dedicated support page to find out how we may be able to support you with any accessibility requirements.