Advanced RNA-Seq and ChiP-Seq Data Analysis
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Date:
Monday 24 - Thursday 27 April 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 21 November 2016Application deadline:
Friday 20 January 2017Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£550Registration 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 and ChIP-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 and ChIP-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.
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 peak calling of ChIP-seq datasets
- Perform alignment and quantification of expression of RNA-seq datasets
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 24 April 2017 | ||
| 09:00 | Arrival and registration | |
| 09:15 | Overview of the course |
Gabriella Rustici |
| 09:45 | Lecture: Introduction to the high-throughput sequencing data analysis workflows | Nicolas Delhomme & Bastian Schiffthaler |
| 10:45 | Tea & coffee break | |
| 11:00 | Lecture: Sequence reads - formats and quality assessment | Nicolas Delhomme & Bastian Schiffthaler |
| 11:45 | Practical: Quality assessment | Nicolas Delhomme & Bastian Schiffthaler |
| 13:00 | Lunch | |
| 14:00 | Lecture: Mapping strategies for sequence reads | Nicolas Delhomme & Bastian Schiffthaler |
| 15:00 | Practical: Mapping | Nicolas Delhomme & Bastian Schiffthaler |
| 15:30 | Tea & coffee break | |
| 15:45 | Practical: Mapping | Nicolas Delhomme & Bastian Schiffthaler |
| 16:30 | Lecture: Alignments - Formats and manipulation | Nicolas Delhomme & Bastian Schiffthaler |
| 17:00 | Practical: Alignments - Formats and manipulation | Nicolas Delhomme & Bastian Schiffthaler |
| 18:00 | Q&A Session | |
| 19:30 | Dinner at Hinxton Hall | |
| Day 2 - Tuesday 25 April 2017 | ||
| 09:00 | Lecture: Annotation - Genes and Genomes | |
| 09:45 | Practical: Annotation - Genes and Genomes | |
| 10:30 | Tea & coffee break | |
| 10:45 | Lecture: Estimating expression - Genes and Transcripts | Nicolas Delhomme & Bastian Schiffthaler |
| 11:30 | Practical: Estimating expression - Genes and Transcripts | Nicolas Delhomme & Bastian Schiffthaler |
| 13:00 | Lunch | |
| 14:00 | Lecture: Differential expression | Charlotte Soneson |
| 15:30 | Tea & coffee break | |
| 15:45 | Lecture: Differential expression + A comparison of methods for differential expression analysis of RNA-seq data | Charlotte Soneson |
| 17:30 | Q&A session | |
| 19:00 | Dinner at Hinxton Hall | |
| Day 3 - Wednesday 26 April 2017 | ||
| 09:00 | Practical: Differential expression with RNA seq | Charlotte Soneson |
| 11:00 | Tea & coffee break | |
| 11:15 | Practical: Differential expression with RNA seq (cont.) | Charlotte Soneson |
| 12:30 | Lunch | |
| 13:30 | Lecture: Downstream analysis | Nicolas Delhomme & Bastian Schiffthaler |
| 14:30 | Tea & coffee break | |
| 14:45 | Practical: Downstream analysis | Nicolas Delhomme & Bastian Schiffthaler |
| 16:30 | Q&A session | |
| 18:00 | Dinner at Hinxton Hall | |
| Day 4 - Thursday 27 April 2017 | ||
| 09:00 | Lecture: Introduction to ChIP-Seq data and analysis | Bori Mifsud & Federico Agostini |
| 10:00 | Lecture: Peak-callers | Bori Mifsud & Federico Agostini |
| 10:30 | Tea & coffee break | |
| 10:45 | Practical: Peak-callers | Bori Mifsud & Federico Agostini |
| 12:30 | Lunch | |
| 13:30 | Practical: ChIP-Seq data analysis with Bioconductor | Bori Mifsud & Federico Agostini |
| 14:30 | Tea & coffee break | |
| 14:45 | Practical: ChIP-Seq data analysis with Bioconductor (cont.) | Bori Mifsud & Federico Agostini |
| 16:00 | Course feedback and wrap up, and delegates to depart | |
| 16:20 | Coach to Cambridge train station | |