Advanced RNA-Seq Analysis

Date:

 Monday 16 Friday 20 April 2018

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday November 03 2017

Application deadline: 

Friday January 19 2018

Participation: 

Open application with selection

Contact: 

Emily Rees

Registration fee: 

£700

Overview

The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from RNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq data under the guidance of the lecturers and teaching assistants.

Audience

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.

Syllabus, tools and resources

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

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

Additional information

We invite participants to bring along a poster to display for the duration of the course. These will serve to facilitate discussion about your research and to convey your reasons for attending the course to others. Posters must be A2 portrait (420mm x 594mm).

Programme

Time Topic Trainer
Day 1 - Monday 16 April 2018
08:30 - 08:45 Registration and tea/coffee  
08:45 - 09:15 Overview of the course Gabriella Rustici
09:15 - 10:15 Lecture: Introduction to the high-throughput sequencing data analysis workflows Nicolas Delhomme & Bastian Schiffthaler
10:15 - 10:30 Tea and coffee break  
10:30 - 11:15 Lecture: Short read representation, manipulation and quality assessment Nicolas Delhomme & Bastian Schiffthaler
11:15 - 12:30 Practical: Quality assessment Nicolas Delhomme & Bastian Schiffthaler
12:30 - 13:30 Lunch   
13:30 - 14:30 Lecture: Pseudo-alignment Nicolas Delhomme & Bastian Schiffthaler
14:30 - 15:00 Practical: Pseudo-alignment Nicolas Delhomme & Bastian Schiffthaler
15:00 - 15:15 Tea and coffee break  
15:15 - 16:15 Lecture: Biological QA Nicolas Delhomme & Bastian Schiffthaler
16:15 - 17:15 Practical: Biological QA Nicolas Delhomme & Bastian Schiffthaler
17:15 - 18:00 Q&A Session  
18:00 - 19:00 Networking in Hinxton Hall Bar  
19:00 Dinner at Wellcome Genome Campus restaurant  
Day 2 - Tuesday 17 April 2018
09:00 - 10:30

Lecture: Differential expression

Charlotte Soneson 
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Lecture: Differential expression + A comparison of methods for differential expression analysis of RNA-seq data

 

Charlotte Soneson

12:30 - 13:30 Lunch  
13:30 - 15:00 Practical: Differential expression with RMA seq  Charlotte Soneson 
15:00 - 15:15 Tea and coffee break   
15:15 - 16:30 Practical: Differential expression with RNA Charlotte Soneson
16:30 - 18:00 Poster session 1   
18:00 - 19:00 Networking in Hinxton Hall Bar  
19:00 Dinner at Wellcome Genome Campus restaurant  
Day 3 - Wednesday 18 April 2018
09:00 - 10:00 Lecture: transcriptome de novo assembly Nicolas Delhomme & Matthew MacManes
10:00 - 10:15 Tea/coffee break  
10:15 - 12:30 Practical: transcriptome de novo assembly Nicolas Delhomme & Matthew MacManes
12:30 - 13:30 Lunch   
13:30 - 15:00 Practical: transcriptome de novo assembly Nicolas Delhomme & Matthew MacManes
15:00 - 15:15 Tea/coffee break  
15:15 - 16:30 Practical: transcriptome de novo assembly Nicolas Delhomme & Matthew MacManes
16:30 - 18:00 Poster session 2  
18:00 - 19:00 Networking in Hinxton Hall Bar  
19:00 Dinner at Wellome Genome Campus restaurant  
Day 4 - Thursday 19 April 2018
09:00 - 10:00 Lecture: Gene Set Enrichment Analysis (GSEA) Nicolas Delhomme & Bastian Schiffthaler
10:00 - 10:15 Tea/coffee break  
10:15 - 12:30 Practical: GSEA  Nicolas Delhomme & Bastian Schiffthaler 
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: Machine learning and network inference Nicolas Delhomme & Bastian Schiffthaler 
14:30 - 15:30 Practical: Downstream analysis Nicolas Delhomme & Bastian Schiffthaler 
15:30 - 15:45 Tea and coffee break   
15:45 - 17:30 Practical: Downsteam analysis (cont.)  Nicolas Delhomme & Bastian Schiffthaler
17:30 - 18:00 Q&A session  
18:00 - 19:00 Networking in Hinxton Hall Bar  
19:00 Dinner at Wellcome Genome Campus restaurant  
Day 5 - Friday 20 April 2018
09:00 - 10:00 Lecture: Single cell sequencing Aaron Lun 
10:00 - 10:15 Tea/coffee break  
10:15 - 12:30 Practical: Single cell sequencing Aaron Lun 
12:30 - 12:40 Course feedback and wrap up  
12:40 - 13:15 Lunch  
13:15 Coach departs to Cambridge train station