Virtual course
Introduction to RNA-seq and functional interpretation
Gain an introduction to the technology, data analysis, tools, and resources used in RNA sequencing and transcriptomics. The content will provide a broad overview of the subject area, and introduce participants to basic analysis of transcriptomics data using the command line. It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data. Topics will be delivered using a mixture of lectures, practical exercises, and open discussions. Computational work during the course will use small, example data-sets; and there will be no opportunity to analyse personal data.
Virtual course
Participants 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 that 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, meaning participants will not require access to a powerful computer or install complex software on their own machines.
Participants will need to be available between the hours of 09:00 – 16:00 hrs GMT each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.
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.
Some experience with R is beneficial. 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 and here are some that may be of help:
To complete the following suggested tutorials you may want to install Ubuntu for Windows Users if you are using a computer with a Windows Operating System.
- Learn Enough Command Line to Be Dangerous - tutorial
- Learn Enough Command Line to Be Dangerous - manipulating files
- Introduction to R tutorials - Programming basics (if you are completing the R tutorials make sure you complete this one first)
- Introduction to R tutorials - Data Visualization Basics
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 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
Course content
During this course you will learn about:
- RNA-seq file formats and basics of experimental design
- 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 de novo approaches
- Introduction to single-cell transcriptomics
- Data resources covered:
Trainers
Simon Andrews
Babraham Institute Vladimir Benes
EMBL Heidelberg Leonardo Collado-Torres
The Lieber Institute for Brain Development Alison Díaz-Cuevas
LIIGH-UNAM Silvie Korena Fexova
EMBL-EBI Victor Flores López
University of Cambridge Otoniel Maya Lucas
Chalmers University of Technology Eliot Ragueneau
EMBL-EBI Ian Sealy
Queen Mary University of London Krishna Kumar Tiwari
EMBL-EBI Liora Vilmovsky
EMBL-EBI
Programme
The programme for this virtual course is currently under development.
All times in the programme are listed in GMT.
Time Topic Trainer Day one – Monday 12 February 2024 09:30 – 10:30 Welcome and course introduction Patricia Carvajal-López 10:30 – 12:00 Sequencing technologies for RNA-Seq Victor Flores López 12:00 – 13:30 Lunch break 13:30 – 14:30 RNA-seq file formats Victor Flores López 14:30 – 15:00 Coffee break 15:00 – 16:30 Data reproducibility: standards and ontologies –lecture and activity Liora Vilmovsky 16:30 – 17:30 Flash talks 17:30 End of day Day two – Tuesday 13 February 2024 09:00 – 10:30 Introduction to RNA-seq Simon Andrews 10:30 – 11:00 Coffee 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 Coffee break 16:00 – 17:30 RNA-seq practical Simon Andrews 17:30 – 18:30 Flash talks 18:30 End of day Day three – Wednesday 14 February 2024 09:00 – 10:30 De novo approaches to RNA-seq Victor Flores López 10:30 – 11:00 Coffee break 11:00 – 12:00 Annotating the genome with RNA-seq data Victor Flores López and Alison Díaz-Cuevas 12:00 – 13:00 Lunch break 13:00 – 14:30 Genome annotation practical Victor Flores López and Alison Díaz-Cuevas 14:30 – 15:00 Coffee break 15:00 – 16:30 Next steps in gene prioritisation Ian Sealy 16:30 – 16:45 Coffee break 16:45 – 18:30 Next steps in gene prioritisation Ian Sealy 18:30 End of day Day four – Thursday 15 February 2024 09:30 – 10:30 Exploring gene expression data Silvie Fexova 10:30 – 11:00 Coffee break 11:00 – 13:00 Toward single-cell sequencing and the Single-Cell Expression Atlas Silvie Fexova and Liora Vilmovsky 13:00 – 14:00 Lunch break 14:00 – 15:30 Back to basics, fundamentals of experimental design Vladimir Benes 15:30 – 16:00 Coffee break 16:00 – 17:00 Reusability of RNA-seq data Leonardo Collado-Torres 17:00 End of day Day five – Friday 16 February 2024 09:15 – 10:30 Exploring biological pathways Krishna Tiwari and Eliot Ragueneau 10:30 – 11:00 Coffee break 11:00 – 12:30 Reporting of bulk-RNA-Seq data analysis Otoniel Maya Lucas 12:30 – 13:30 Lunch break 13:30 – 14:30 Lecture TBA (ncRNAs, or metadata exercise, or longer practical on Galaxy) TBA 14:30 – 16:00 Graphical tools to explore data TBA 16:00 – 16:30 Course wrap-up Patricia Carvajal-López 16:30 End of day
The programme is currently under development and is subject to minor changes. Please see the 2023 iteration for a reference of the potential content of this course.
Please read our support page before starting your application. In order to be considered for a place on this course, you must do the following:
- Complete the online application form.
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
- Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.
Please submit all documents during the application process by 23:59 on 29 October 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 20 November 2023. If you have any questions regarding the application process please contact Juanita Riveros.
Course materials
The course materials from the 2023 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.
Flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.
Babraham Institute
EMBL Heidelberg
The Lieber Institute for Brain Development
LIIGH-UNAM
EMBL-EBI
University of Cambridge
Chalmers University of Technology
EMBL-EBI
Queen Mary University of London
EMBL-EBI
EMBL-EBI
Programme
The programme for this virtual course is currently under development.
All times in the programme are listed in GMT.
Time | Topic | Trainer |
Day one – Monday 12 February 2024 | ||
09:30 – 10:30 | Welcome and course introduction | Patricia Carvajal-López |
10:30 – 12:00 | Sequencing technologies for RNA-Seq | Victor Flores López |
12:00 – 13:30 | Lunch break | |
13:30 – 14:30 | RNA-seq file formats | Victor Flores López |
14:30 – 15:00 | Coffee break | |
15:00 – 16:30 | Data reproducibility: standards and ontologies –lecture and activity | Liora Vilmovsky |
16:30 – 17:30 | Flash talks | |
17:30 | End of day | |
Day two – Tuesday 13 February 2024 | ||
09:00 – 10:30 | Introduction to RNA-seq | Simon Andrews |
10:30 – 11:00 | Coffee 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 | Coffee break | |
16:00 – 17:30 | RNA-seq practical | Simon Andrews |
17:30 – 18:30 | Flash talks | |
18:30 | End of day | |
Day three – Wednesday 14 February 2024 | ||
09:00 – 10:30 | De novo approaches to RNA-seq | Victor Flores López |
10:30 – 11:00 | Coffee break | |
11:00 – 12:00 | Annotating the genome with RNA-seq data | Victor Flores López and Alison Díaz-Cuevas |
12:00 – 13:00 | Lunch break | |
13:00 – 14:30 | Genome annotation practical | Victor Flores López and Alison Díaz-Cuevas |
14:30 – 15:00 | Coffee break | |
15:00 – 16:30 | Next steps in gene prioritisation | Ian Sealy |
16:30 – 16:45 | Coffee break | |
16:45 – 18:30 | Next steps in gene prioritisation | Ian Sealy |
18:30 | End of day | |
Day four – Thursday 15 February 2024 | ||
09:30 – 10:30 | Exploring gene expression data | Silvie Fexova |
10:30 – 11:00 | Coffee break | |
11:00 – 13:00 | Toward single-cell sequencing and the Single-Cell Expression Atlas | Silvie Fexova and Liora Vilmovsky |
13:00 – 14:00 | Lunch break | |
14:00 – 15:30 | Back to basics, fundamentals of experimental design | Vladimir Benes |
15:30 – 16:00 | Coffee break | |
16:00 – 17:00 | Reusability of RNA-seq data | Leonardo Collado-Torres |
17:00 | End of day | |
Day five – Friday 16 February 2024 | ||
09:15 – 10:30 | Exploring biological pathways | Krishna Tiwari and Eliot Ragueneau |
10:30 – 11:00 | Coffee break | |
11:00 – 12:30 | Reporting of bulk-RNA-Seq data analysis | Otoniel Maya Lucas |
12:30 – 13:30 | Lunch break | |
13:30 – 14:30 | Lecture TBA (ncRNAs, or metadata exercise, or longer practical on Galaxy) | TBA |
14:30 – 16:00 | Graphical tools to explore data | TBA |
16:00 – 16:30 | Course wrap-up | Patricia Carvajal-López |
16:30 | End of day |
The programme is currently under development and is subject to minor changes. Please see the 2023 iteration for a reference of the potential content of this course.
Please read our support page before starting your application. In order to be considered for a place on this course, you must do the following:
- Complete the online application form.
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
- Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.
Please submit all documents during the application process by 23:59 on 29 October 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 20 November 2023. If you have any questions regarding the application process please contact Juanita Riveros.
Course materials
The course materials from the 2023 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.
Flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.