Virtual course

Introduction to RNA-seq and functional interpretation

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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:

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:

Trainers

Tom Hancocks
EMBL-EBI
Jonathan Manning
EMBL-EBI
Chandra Chilamakuri
CRUK Cambridge Institute
Leanne Haggerty
EMBL-EBI
Jamie Allen
EMBL-EBI
Carlos Garcia Giron
EMBL-EBI
Kostas Billis
EMBL-EBI
Simon Andrews
Babraham Institute
Liis Kolberg
University of Tartu
Nancy George
EMBL-EBI
Irene Papatheodorou
EMBL-EBI
Thawfeek Varusai
EMBL-EBI
Andrew Hercules
EMBL-EBI
Anton Petrov
EMBL-EBI
Blake Sweeney
EMBL-EBI

Programme

Day 1 - Tuesday 16 March

Time Topic Trainer
09:30-09:45 Arrival, check-in, and hangout Tom Hancocks & Meredith Wilmott
09:45-10:00 Introduction to virtual training Tom Hancocks
10:00-10:30 Participant introductions and networking Tom Hancocks
10:30-10:45 Break  
10:45-12:30 Experimental design for RNA-seq - lecture, and activity Chandra Chilamakuri
12:30-13:30 Break  
13:30-15:00 RNA-seq file formats Jonathan Manning
15:00-15:15 Break  
15:15-16:30 Data reproducibility: standards and ontologies - lecture and activity Nancy George
16:30-17:00 Flash presentations All
17:00 End of day  

Day 2 - Wednesday 17 March

Time Topic Trainer
09:30-09:45 Arrival, check-in, and hangout Tom Hancocks & Meredith Wilmott
09:45-10:00 Group activity All
10:00-10:30 Annotating the genome with RNA-seq data Leanne Haggerty & Genebuild Team
10:30-11:30 Genome annotation practical Leanne Haggerty & Genebuild Team
11:30-12:30 Introduction to RNA-seq Simon Andrews
12:30-13:30 Break  
13:30-15:30 RNA-seq practical Simon Andrews
15:30-15:45 Break  
15:45-16:30 RNA-seq practical Simon Andrews
16:30-17:00 Flash presentations All
17:00 End of day  

Day 3 - Thursday 18 March

Time Topic Trainer
09:30-09:45 Arrival, check-in, and hangout Tom Hancocks & Meredith Wilmott
09:45-10:00 Group activity All
10:00-11:45 Next steps in gene prioritisation Liis Kolberg
11:45-12:00 Break  
12:00-13:00 Next steps in gene prioritisation Liis Kolberg
13:00-14:00 Break  
14:00-15:00 Exploring gene expression data Nancy George
15:00-15:15 Break  
15:15-16:30 Exploring gene expression data Nancy George
16:30-17:00 Flash presentations All

Day 4 - Friday 19 March

Time Topic Trainer
09:30-09:45 Arrival, check-in, and hangout Tom Hancocks & Meredith Wilmott
09:45-10:00 Group activity All
10:00:11:00 Toward single-cell sequencing Irene Papatheodorou
11:00-11:15 Break  
11:15-12:15 Exploring biological pathways Thawfeek Varusai
12:15-13:15 Break  
13:15-14:15 Open Targets Platform: integrating human data for drug discovery Andrew Hercules
14:15-15:00 Galaxy workflows for non-coding RNA Anton Petrov & Blake Sweeney
15:00-15:30 Single-cell Expression Atlas Nancy George
15:30-16:00 Course wrap-up and feedback All
16:00 End of course  

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.

This course has ended

16 - 19 March 2021
£160.00
Contact
Meredith Wilmott

Organisers
  • Tom Hancocks
    EMBL-EBI
  • Irene Papatheodorou
    EMBL-EBI

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