Course at EMBL-EBI
Introduction to RNA-seq and functional interpretation
This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. The content is intended to provide a broad overview of the subject area, and to introduce participants to simple data analysis using the command line and APIs. It will also highlight key resources, approaches and methodologies to begin the biological interpretation and analysis of transcriptomics data. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets - there will be no opportunity to analyse personal data.
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
- Use a range of bioinformatics software and tools to undertake basic 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:
Trainers
Tom Hancocks
EMBL-EBI, UK Malwina Prater
University of Cambridge, UK Suhaib Mohammed
EMBL-EBI, UK Silvie Fexova
EMBL-EBI, UK Pablo Moreno
EMBL-EBI, UK Kostas Billis
EMBL-EBI, UK Leanne Haggerty
EMBL-EBI, UK Jamie Allen
EMBL-EBI, UK Denye Ogeh
EMBL-EBI, UK Simon Andrews
Babraham Institute, UK Liis Kolberg
University of Tartu, Estonia Denise Carvalho-Silva
EMBL-EBI, UK Thawfeek Mohamed Varusai
EMBL-EBI, UK Asier Gonzalez
EMBL-EBI, UK Irene Papatheodorou
EMBL-EBI, UK Anton Petrov
EMBL-EBI, UK Blake Sweeney
EMBL-EBI, UK
Programme
Day 1: Tuesday 21 January 2020
12:00-13:00
Arrival, registration, lunch
13:00-14:00
Welcome, introductions and networking
Tom Hancocks
14:00-15:30
Experimental design for RNA-Seq
Malwina Prater
15:30-16:00
Break
16:00-17:00
RNA-Seq file formats
Suhaib Mohammed
17:00-18:00
Data reproducibility: standards and ontologies
Silvie Fexova
18:00
End of day
19:00
Evening meal
Hinxton Hall Restaurant
20:30
Shuttle to Holiday Inn, Duxford
Day 2 – Wednesday 22 January 2020
08:30
Shuttle to campus
08:45
Arrival
09:00-10:30
Annotating the genome with RNA-Seq data
Leanne Haggerty & Kostas Billis
10:30-11:00
Break
11:00-12:30
Introduction to RNA-Seq
Simon Andrews
12:30-13:30
Lunch
13:30-16:00
RNA-Seq practical
Simon Andrews
16:00-16:30
Break
16:30-18:30
Exploring gene expression data with Expression Atlas
Silvie Fexova
18:30
End of day
19:00
Evening meal
Hinxton Hall Restaurant
20:30
Shuttle to Holiday Inn, Duxford
Day 3 – Thursday 23 January 2020
08:30
Shuttle to campus
08:45
Arrival
09:00-11:00
Next steps in gene prioritisation
Liis Kolberg
11:00-11:30
Break
11:30-12:30
Next steps in gene prioritisation
Liis Kolberg
12:30-13:30
Lunch
13:30-15:30
Open Targets Platform: integrating human data for drug discovery
Denise Carvalho-Silva & Asier Gonzalez
15:30-16:00
Break
16:00-17:00
Towards single-cell RNA sequencing
Irene Papatheodorou
17:70-18:30
Challenges in single-cell sequencing analysis
Wendi Bacon
18:30
End of day
18:45
Evening meal
Red Lion Pub, Hinxton
21:00
Shuttle to Holiday Inn, Duxford
Day 4 – Friday 24 January 2020
08:15
Checkout of accommodation
08:30
Shuttle to campus
08:45
Arrival
09:00-10:00
Exploring biological pathways
Thawfeek Varusai
10:00-11:00
Galaxy workflows for non-coding RNA
Anton Petrov & Blake Sweeney
11:00-11:30
Break
11:30-12:30
Galaxy workflows for non-coding RNA
Anton Petrov & Blake Sweeney
12:30-12:45
Course wrap-up and feedback
12:45-13:30
Lunch
13:30
End of course
13:45
Shuttle to Station Road, Cambridge
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
- Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
- Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course
Please submit all documents to Marina Pujol (mpuljo@ebi.ac.uk) by 12:00 GMT on Friday 4 October, 2019.
Incomplete applications will not be considered.
EMBL-EBI, UK
University of Cambridge, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Babraham Institute, UK
University of Tartu, Estonia
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Programme
Day 1: Tuesday 21 January 2020 |
||
---|---|---|
12:00-13:00 | Arrival, registration, lunch | |
13:00-14:00 | Welcome, introductions and networking | Tom Hancocks |
14:00-15:30 | Experimental design for RNA-Seq | Malwina Prater |
15:30-16:00 | Break | |
16:00-17:00 | RNA-Seq file formats | Suhaib Mohammed |
17:00-18:00 | Data reproducibility: standards and ontologies | Silvie Fexova |
18:00 | End of day | |
19:00 | Evening meal | Hinxton Hall Restaurant |
20:30 | Shuttle to Holiday Inn, Duxford |
Day 2 – Wednesday 22 January 2020 |
||
---|---|---|
08:30 | Shuttle to campus | |
08:45 | Arrival | |
09:00-10:30 | Annotating the genome with RNA-Seq data | Leanne Haggerty & Kostas Billis |
10:30-11:00 | Break | |
11:00-12:30 | Introduction to RNA-Seq | Simon Andrews |
12:30-13:30 | Lunch | |
13:30-16:00 | RNA-Seq practical | Simon Andrews |
16:00-16:30 | Break | |
16:30-18:30 | Exploring gene expression data with Expression Atlas | Silvie Fexova |
18:30 | End of day | |
19:00 | Evening meal | Hinxton Hall Restaurant |
20:30 | Shuttle to Holiday Inn, Duxford |
Day 3 – Thursday 23 January 2020 |
||
---|---|---|
08:30 | Shuttle to campus | |
08:45 | Arrival | |
09:00-11:00 | Next steps in gene prioritisation | Liis Kolberg |
11:00-11:30 | Break | |
11:30-12:30 | Next steps in gene prioritisation | Liis Kolberg |
12:30-13:30 | Lunch | |
13:30-15:30 | Open Targets Platform: integrating human data for drug discovery | Denise Carvalho-Silva & Asier Gonzalez |
15:30-16:00 | Break | |
16:00-17:00 | Towards single-cell RNA sequencing | Irene Papatheodorou |
17:70-18:30 | Challenges in single-cell sequencing analysis | Wendi Bacon |
18:30 | End of day | |
18:45 | Evening meal | Red Lion Pub, Hinxton |
21:00 | Shuttle to Holiday Inn, Duxford |
Day 4 – Friday 24 January 2020 |
||
---|---|---|
08:15 | Checkout of accommodation | |
08:30 | Shuttle to campus | |
08:45 | Arrival | |
09:00-10:00 | Exploring biological pathways | Thawfeek Varusai |
10:00-11:00 | Galaxy workflows for non-coding RNA | Anton Petrov & Blake Sweeney |
11:00-11:30 | Break | |
11:30-12:30 | Galaxy workflows for non-coding RNA | Anton Petrov & Blake Sweeney |
12:30-12:45 | Course wrap-up and feedback | |
12:45-13:30 | Lunch | |
13:30 | End of course | |
13:45 | Shuttle to Station Road, Cambridge |
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
- Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
- Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course
Please submit all documents to Marina Pujol (mpuljo@ebi.ac.uk) by 12:00 GMT on Friday 4 October, 2019.
Incomplete applications will not be considered.