RNA-Sequence Analysis

Date:

 Monday 8 Friday 12 April 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Wednesday October 10 2018

Application deadline: 

Friday January 11 2019

Participation: 

First come, first served

Contact: 

Frank O’Donnell

Registration fee: 

£1000

Overview

This course aims to 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.

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

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 in the Wellcome Genome Campus Conference Centre Monday-Friday inclusive. Please contact the Conference Centre directly if you wish to arrange to stay Sunday-Monday. The course includes breakfast and evening meals at Hinxton Hall, and breaks and lunches outside the EMBL-EBI training rooms.

Programme

Time Topic Trainer
Day 1 - Monday 8 April 2019
09:00 - 09:15 Arrival and registration  
09:00 - 09:30 Overview of the course Gabriella Rustici
09:30 - 10:30 Introduction to the high-throughput sequencing data analysis workflows Nicolas Delhomme & Bastian Schiffthaler
10:30 - 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 - 13:00 Lunch and posters  
13:00 - 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  
18:00 - 19:30 Check-in at Conference Centre and discussion Hinxton Hall Bar
19:30 Evening meal Hinxton Hall Restaurant
Day 2 - Tuesday 9 April 2019
08:45 Arrival  
09:00 - 10:30 Differential expression To be confirmed
10:30 - 10:45 Break  
10:45 - 12:30 Differential expression; Comparison of methods for differential expression analysis of RNA-Seq data To be confirmed
12:30 - 13:30 Lunch and posters  
13:30 - 15:00 Differential expression with RNA-Seq practical To be confirmed
15:00 - 15:15 Break   
15:15 - 16:30 Differential expression with RNA-Seq practical To be confirmed
16:30 - 18:00 Poster session - odd numbers   
18:00 - 19:00 Discussion Hinxton Hall Bar
19:00 Evening meal Hinxton Hall Restaurant
Day 3 - Wednesday 10 April 2019
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 Poster session - even numbers  
18:00 - 19:00 Discussion Hinxton Hall Bar
19:00 Dinner at Wellome Genome Campus restaurant Hinxton Hall Restaurant
Day 4 - Thursday 11 April 2019
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  
18:00 - 19:00 Discussion Hinxton Hall Bar
19:00 Evening meal Hinxton Hall Restaurant
Day 5 - Friday 12 April 2019
08:30 Check out of Conference Centre  
08:45 Arrival  
09:00 - 10:00 Single cell sequencing Aaron Lun 
10:00 - 10:15 Break  
10:15 - 12:30 Single cell sequencing practical Aaron Lun 
12:30 - 12:45 Feedback and wrap up  
12:45 - 13:15 Lunch  
13:15 Coach to Cambridge Station