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 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 09:30-16:00 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:

  • RNA-Seq file formats and basics of experimental 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

Trainers

Simon Andrews
Babraham Institute
Helena Cornu
EMBL-EBI
Selene L. Fern√°ndez-Valverde
CINVESTAV-LANGEBIO
Nancy George
EMBL-EBI
Andrew Hercules
EMBL-EBI
Liis Kolberg
University of Tartu
Jonathan Manning
EMBL-EBI
Irene Papatheodorou
EMBL-EBI
Konstantinos Tsirigos
EMBL-EBI
Eliot Ragueneau
EMBL-EBI
Silvie Korena Fexova
EMBL-EBI
Victor Flores
University of Cambridge
Krishna Kumar Tiwari
EMBL-EBI

Programme

All times given in GMT

The session times may change between now and when the course takes place

 

Time

Subject

Trainer

Day 1 - Monday 21 February

09:30-09:45

Arrival, check-in, and hangout

 

09:45-10:00

Introduction to virtual training

Patricia Carvajal-Lopez

10:00-10:30

Participant introductions and networking

All

10:30-10:45

Break

 

10:45-12:30

Experimental design for RNA-seq - lecture, and activity

Selene Fernandez

12:30-13:30

Lunch break

 

13:30-14:00

Flash talks

 

14:00-14:50

RNA-seq file formats

Jonathan Manning

14:50-15:00

Break

 

15:00-16:00

Data reproducibility: Standards and ontologies - lecture and activity

Silvie Fexova

16:00

End of day

 

Day 2 - Tuesday 22 February

09:30 -11:00

Introduction to RNA-seq

Simon Andrews

11:00-11:10

Break

 

11:10-13:10

RNA-seq practical

Simon Andrews

13:10-14:00

Lunch break

 

14:00-16:30

RNA-seq practical

Simon Andrews

16:30-16:40

Break

 

16:40-18:00

De novo approach to RNA-seq

Selene Fernandez

18:00

End of day

 

Day 3 - Wednesday 23 February

09:30-10:00

Arrival, check-in, and hangout

Patricia Carvajal-Lopez, Meredith Willmot

10:00-11:00

Annotating the genome with RNA-seq data


Victor Flores

11:00-11:10

Break

 

11:10-12:30

Genome annotation practical

Victor Flores

12:30-13:30

Lunch break

 

13:30-14:00

Flash talks

All

14:00-16:20

Next steps in gene prioritisation

Liis Kolberg

16:20-16:30

Break

 

16:30-17:30

Next steps in gene prioritisation

Liis Kolberg

17:30

End of day

 

Day 4 - Thursday 24 February

09:30-10:00

Arrival, check-in, and hangout

Patricia Carvajal-Lopez, Meredith Willmot

10:00-11:30

Exploring gene expression data

Nancy George

11:30-11:40

Break

 

11:40-13:00

Exploring gene expression data

Nancy George

13:00-14:00

Lunch break

 

14:00-14:30

Flash talks

All

14:30-16:00

Toward single-cell sequencing

Irene Papatheodorou

16:00-16:10

Break

 

16:10-17:30

Single-cell Expression Atlas

Silvie Fexova

17:30

End of day

 

Day 5 - Friday 25 February

09:55-10:00

Arrival

Patricia Carvajal-Lopez, Meredith Willmot

10:00-11:00

Exploring biological pathways

Eliot Ragueneau, Krishna Tiwari

11:00-11:15

Break

 

11:15-12:15

Open Targets Platform: Integrating human data for drug discovery

Helena Cornu, Konstantinos Tsirigos, Andrew Hercules

12:15-13:15

Lunch Break

 

13:15-13:45

Flash talks

All

13:45-14:15 Group activity Patricia Carvajal-Lopez, Meredith Willmot
14:15-14:30 Break & group photo  

14:30-16:00

Galaxy workflows for non-coding RNA

Selene Fernandez

16:00-16:30

Course wrap-up and feedback

Patricia Carvajal-Lopez

16:30

End of Course

 

Please read our page on application advice 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 providing answers as directed
  • 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 26 November 2021.  

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 10 December 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.

This course has ended

21 - 25 February 2022
£200.00
Contact
Meredith Willmott

Organisers
  • Irene Papatheodorou
    EMBL-EBI
  • Patricia Carvajal Lopez
    EMBL-EBI
  • Selene L. Fernandez-Valverde
    Cinvestav-LANGEBIO

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