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 communication via Slack. 

Pre-recorded material will be made available to registered participants prior to the start of the course and 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 09:30-17:30 GMT each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis 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.

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:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
• Basic R concept tutorials: www.r-tutor.com/r-introduction

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
• 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 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:
  • Expression Atlas
  • Single-cell Expression Atlas
  • g:Profiler
  • Open Targets Platform
  • Reactome
  • RNAcentral

Trainers

Please read our page on application advice before starting. 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 "application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography
  • work history
  • current research interests
• Upload a 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 midnight on Friday 22nd January 2021.  

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 05th February 2021. If you have any questions regarding the application process please contact Meredith Willmott (meredith@ebi.ac.uk). 

Participant 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. Further details will be provided following registration

Participant scientific poster

There will be an additional opportunity for all participants to submit a poster which will be shared with the trainers and other participants alongside a scientific biography. The poster is an opportunity to provide further information about their research and stimulate more discussions between course participants. Further details will be provided following registration.