Course at EMBL-EBI

RNA-sequence analysis

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

This course will familiarise participants with advanced data analysis methodologies in the field of transcriptomics and to provide practical training in the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from RNA-Seq experiments and illustrate different ways of analysing the generated data. Practicals will enable participants to apply statistical methods to the analysis of RNA-Seq data under the guidance of the trainers.

Who is this course for?

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.

What will I learn?

Learning outcomes

After this course you should be able to:

• Understand the advantages and limitations of the high-throughput assays presented
• Assess the quality of your datasets
• Understand the difference between short read aligners
• Perform alignment and quantification of expression of RNA-seq datasets
• Understand the challenges of single cell sequencing analysis

Course content

During this course you will learn about:

  • High-throughput sequencing technology
  • Quality control of raw reads: FASTQC and fastx toolkit
  • Considerations on experiment design for RNA-seq
  • Read pseudoalignment and quantification: kallisto, salmon
  • Differential expression analysis and differential exon usage: R, edgeR, DESeq2, DEXSeq
  • Downstream DE data processing and gene target discovery
  • Single cell RNA-seq analysis: scran, scater

Trainers

Gabriella Rustici
University of Cambridge, UK
Nicolas Delhomme
UPSC, Umeå, Sweden
Charlotte Soneson
University of Zurich, Switzerland
Bastian Schiffthaler
Umeå University, Sweden
Matthew Macmanes
University of New Hampshire, USA
Ximena Ibarra-Soria
EMBL-EBI, UK

Programme

Day 1 – Monday 8 April 2019
08:30 - 09:30 Arrival and registration  
09:30 - 09:45 Overview of the course Gabriella Rustici
09:45 - 10:45 Introduction to the high-throughput sequencing data analysis workflows Nicolas Delhomme & Bastian Schiffthaler
10:45 - 11:00 Break  
11:00 - 11:45 Short read representation, manipulation and quality assessment Nicolas Delhomme & Bastian Schiffthaler
11:45 - 13:00 Quality assessment practical Nicolas Delhomme & Bastian Schiffthaler
13:00 - 14:00 Lunch and posters  
14:00 - 15:00 Pseudo-alignment Nicolas Delhomme & Bastian Schiffthaler
15:00 - 15:30 Pseudo-alignment practical Nicolas Delhomme & Bastian Schiffthaler
15:30 - 15:45 Break  
15:45 - 16:45 Biological quality assessment Nicolas Delhomme & Bastian Schiffthaler
16:45 - 17:45 Biological quality assessment practical Nicolas Delhomme & Bastian Schiffthaler
17:45 - 18:00 Q&A Session  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 2 – Tuesday 9 April 2019
08:00 Shuttle to Wellcome Genome Campus  
08:45 Arrival  
09:00 - 10:30 Differential expression Charlotte Soneson
10:30 - 10:45 Break  
10:45 - 12:30 Differential expression; Comparison of methods for differential expression analysis of RNA-Seq data Charlotte Soneson
12:30 - 13:30 Lunch and posters  
13:30 - 15:00 Differential expression with RNA-Seq practical Charlotte Soneson
15:00 - 15:15 Break  
15:15 - 16:30 Differential expression with RNA-Seq practical Charlotte Soneson
16:30 - 18:00 Discussion  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 3 – Wednesday 10 April 2019
08:00 Shuttle to Wellcome Genome Campus  
08:45 Arrival  
09:00 - 10:00 Transcriptome de novo assembly Nicolas Delhomme & Matthew MacManes
10:00 - 10:15 Break  
10:15 - 12:30 Transcriptome de novo assembly practical Nicolas Delhomme & Matthew MacManes
12:30 - 13:30 Lunch and posters  
13:30 - 15:00 Transcriptome de novo assembly practical Nicolas Delhomme & Matthew MacManes
15:00 - 15:15 Break  
15:15 - 16:30 Transcriptome de novo assembly practical Nicolas Delhomme & Matthew MacManes
16:30 - 18:00 Discussion  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 4 – Thursday 11 April 2019
08:00 Shuttle to Wellcome Genome Campus  
08:45 Arrival  
09:00 - 10:00 Gene Set Enrichment Analysis (GSEA) Nicolas Delhomme & Bastian Schiffthaler
10:00 - 10:15 Break  
10:15 - 12:30 GSEA practical Nicolas Delhomme & Bastian Schiffthaler 
12:30 - 13:30 Lunch and posters  
13:30 - 14:30 Machine learning and network inference Nicolas Delhomme & Bastian Schiffthaler 
14:30 - 15:30 Downstream analysis practical Nicolas Delhomme & Bastian Schiffthaler 
15:30 - 15:45 Break  
15:45 - 17:30 Downstream analysis practical Nicolas Delhomme & Bastian Schiffthaler
17:30 - 18:00 Q&A session  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Holiday Inn, Impington  
Day 5 – Friday 12 April 2019
07:45 Check out of accommodation  
08:00 Shuttle to Wellcome Genome Campus  
08:45 Arrival  
09:00 - 10:00 Single cell sequencing Ximena Ibarra-Soria
10:00 - 10:15 Break  
10:15 - 12:30 Single cell sequencing practical Ximena Ibarra-Soria
12:30 - 12:45 Feedback and wrap up Tom Hancocks
12:45 - 13:15 Lunch  
13:15 Shuttle to Cambridge Station  

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:

  1. Complete the online application form
  2. 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
  3. 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 Frank O'Donnell (frank@ebi.ac.uk) by 12:00 GMT on Friday 11 January, 2019.

Incomplete applications will not be considered.

Participants have the opportunity to display an A2 (420x594mm - portrait) poster for the duration of the course. We will ask you to submit your poster before the course for printing on site. It is not possible to display posters of a different size or orientation.

Accommodated will be provided at the Holiday Inn, Impington Monday-Friday inclusive. This location is difficult to access from both the Wellcome Genome Campus or Cambridge and we strongly recommend that successful participants consider finding alternative accommodation close to Cambridge Station prior to or after the course to ease journeys. Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates.

The course includes evening meals at the Hinxton Hall Restaurant on campus, and breaks and lunches outside the EMBL-EBI training rooms.

Find similar courses
This course has ended

08 - 12 April 2019
European Bioinformatics Institute United Kingdom
£1000
Contact
Marina Pujol

Organisers
  • Tom Hancocks
    EMBL-EBI, UK
  • Gabriella Rustici
    University of Cambridge, UK

Share this event with: