ENGAGE/GEUVADIS RNA-seq Course
Is it right for me?
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. The aim of this course is to familiarize the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches.
What will I learn?
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.
Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.
What will it cover?
The course covers data analysis of RNA-Seq experiments.
Topics will include: short read alignment, data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.
| Time | Topic | |
|---|---|---|
|
Day 1 - Monday 12th September 2011 |
||
| 08:30 | Coach collection from Jesus College to EBI | |
| 09:00 - 09:30 | Registration - Welcome & Safety | |
| 09:30 - 10:30 | Lecture: Introduction to RNA-seq technology | Peter ‘t Hoen |
| 10:30 - 10:45 | Tea/Coffee Break | |
| 10:45 - 12:00 | Lecture: Overview of R/Bioconductor packages for short read analysis | Angela Goncalves |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 15:30 | Practical: Reading and manipulating short reads starting from SAM file, visualize alignments and coverage vectors, make quality-related plots |
Angela Goncalves |
| 15:30 - 15:45 | Tea/Coffee Break | |
| 15:45 - 17:00 | Lecture/demo: ArrayExpressHTS | Angela Goncalves |
| 17:00 | Coach collection from EBI to Jesus College Cambridge | |
| 19:30 - 22:00 | Course Dinner Jesus College | |
|
Day 2 - Tuesday 13th September 2011 |
||
| 08:30 | Coach collection from Jesus College to EBI | |
| 09:00 - 10:00 | Lecture: Differential expression in count data | Thomas J. Hardcastle |
| 10:00 - 10:15 | Tea/Coffee Break | |
| 10:15 - 12:30 | Practical: Differential expression in count data with baySeq | Thomas J. Hardcastle |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:30 | Practical: Differential gene expression with edgeR | Peter ‘t Hoen |
| 15:30 - 15:45 | Tea/Coffee Break | |
| 15:45 - 17:00 | Lecture: Archiving RNA-seq data | Gabriella Rustici |
| 17:00 | Coach collection from EBI to Jesus College Cambridge | |
This event is co-sponsored by ENGAGE/GEUVADIS/EBI. Registration is free but there will be a selection process and you will be notfied by 19th August if your appication has been successful.
It includes:
* Accommodation and Breakfast for 3 nights at Jesus College
* (check in 11th September 2011, check out 14th September 2011)
* Transport to/from the accommodation and the EBI during the 2 days
* Refreshments and lunch during the course
* Course Dinner on Monday evening at Jesus College
* Course materials
* Use of EBI IT Training Room computer during the 2 day course All delegates will need to arrange their own travel to and from the course.
Invited Speakers:
- Peter ‘t Hoen, Leiden University Medical Center, Netherlands
- Angela Goncalves, EBI-EMBL, UK
- Mar Gonzales Porta, EBI-EMBL, UK
- Thomas J. Hardcastle, Cambridge University, UK
- Gabriella Rustici, EBI-EMBL, UK
The course materials are available from the following link:
/training/sites/ebi.ac.uk.training/files/materials/2011/engage_september.zip