Advanced RNA-Seq and ChiP-Seq Data Analysis 2016
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Date:
Monday 18 - Thursday 21 April 2016Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Wednesday 25 November 2015Application deadline:
Friday 26 February 2016Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£550.00 - (Including 3 nights accommodation, breakfasts, teas/coffees, lunches and evening meals)Registration 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 18 April 2016 | ||
| 08:15 | Registration | |
| 08:30 | Overview of the course | Gabriella Rustici |
| 09:15 | Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R |
Nicolas Delhomme |
| 10:15 | Tea & coffee break | |
| 10:30 | Lecture/Practical: Short read representation, manipulation and quality assessment | Nicolas Delhomme |
| 11:30 | Lecture/Practical: Genes and Genomes | Nicolas Delhomme |
| 12:30 | Lunch | |
| 13:30 | Lecture/Practical: Genes and Genomes (continued) | Nicolas Delhomme |
| 14:00 | Lecture: Mapping strategies for sequence reads | Ernest Turro |
| 15:00 | Tea & coffee break | |
| 15:15 | Practical Mapping | Ernest Turro |
| 17:30 | Q&A Session | |
| 19:30 | Dinner at the Red Lion Pub, Hinxton | |
| Day 2 - Tuesday 19 April 2016 | ||
| 09:00 | Lecture: Representing and manipulating alignments | Nicolas Delhomme |
| 09:45 | Practical: Representing and manipulating alignments | Nicolas Delhomme |
| 10:30 | Tea & coffee break | |
| 10:45 | Practical: Representing and manipulating alignments | Nicolas Delhomme |
| 12:30 | Lunch | |
| 13:30 | Lecture: Estimating expression over genes and exons | Nicolas Delhomme |
| 14:30 | Practical: Estimating expression over genes and exons | Nicolas Delhomme |
| 15:30 | Tea & coffee break | |
| 15:45 | Practical: Discovering novel transcribed regions | Nicolas Delhomme |
| 16:30 | Working without a reference genome | Nicolas Delhomme |
| 17:30 | Q&A session | Nicolas Delhomme |
| 19:30 | Dinner at Hinxton Hall | |
| Day 3 - Wednesday 20 April 2016 | ||
| 09:00 | Lecture: Normalizing RNA-seq data | Bori Mifsud & Federico Agostini |
| 10:00 | Lecture: Differential expression | Bori Mifsud & Federico Agostini |
| 11:00 | Tea & coffee break | |
| 11:15 | Lecture: Multiple testing | Bori Mifsud & Federico Agostini |
| 12:30 | Lunch | |
| 13:30 | Practical: Differential expression with RNA seq | Bori Mifsud & Federico Agostini |
| 15:30 | Tea & coffee break | |
| 15:45 | Practical: Differential expression with RNA seq (cont.) | Bori Mifsud & Federico Agostini |
| 17:30 | Q&A session | |
| 17:45 | Lecture: Single Cell sequencing | John Marioni |
| 19:30 | Dinner at Hinxton Hall | |
| Day 4 - Thursday 21 April 2016 | ||
| 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 | Bori Mifsud & Federico Agostini |
| 16:00 | Course feedback and wrap up, and delegates to depart | |
| 16:20 | Coach to Cambridge train station | |
In association with
How to apply
In order to be considered for a place on this course, applicants must do the following:
- Complete the online application form.
- Submit a PDF document to johanna@ebi.ac.uk containing a short biography including your work history, a description of your current research interests and a short biography. Each document should be no longer than 100 words.
- Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.
Further details will be provided on your confirmation email after completing the online form.
Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.
Application deadline
26 February 2016
Number of places
30 places
Organisers
Gabriella Rustici - University of Cambridge, UK
Trainers
Gabriella Rustici - University of Cambridge, UK
Nicolas Delhomme - UPSC, Umeå, Sweden
John Marioni - EMBL-EBI, UK
Federico Agostini - Crick Institute, London
Bori Mifsud - Queen Mary University, London
Ernest Turro - University of Cambridge
Bastian Schiffthaler - Umeå University, Sweden