Advanced RNA-Seq Analysis
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Date:
Monday 16 - Friday 20 April 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 03 November 2017Application deadline:
Friday 19 January 2018Participation:
Open application with selectionContact:
Emily ReesRegistration fee:
£700Registration closed
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 |