ENGAGE/GEUVADIS RNA-seq Workshop 2012
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 - Tuesday 04 December 2012 | |
| 09:00 - 09:30 | Registration - Course Materials part 1 Course Materials part 2 |
| 09:30 - 10:30 | Lecture: Introduction to RNA-seq technology - Peter ‘t Hoen (LUMC) |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:00 | Lecture: Dealing with raw reads: quality assessment and filtering - Mar Gonzalez-Porta (EBI) |
| 12:00 - 13:00 | Lunch |
| 13:00 - 14:30 | Practical: Dealing with raw reads: quality assessment and filtering - Mar Gonzalez-Porta (EBI) |
| 14:30 - 15:30 | Lecture: RNA alignment tools - Paolo Ribeca (CNAG) |
| 15:30 - 15:45 | Coffee Break |
| 15:45 - 17:30 | Practical: RNA alignment and visualization - Paolo Ribeca (CNAG)/Peter 't Hoen (LUMC) |
| 19:00 | Dinner at St John's College, Cambridge - Sponsored by CAGE-KID |
| Day 2 - Wednesday 05 December 2012 | |
| 09:00 - 10:00 | Lecture: Introduction to RNA-Seq data and analysis - John Marioni (EBI) |
| 10:00 - 10:30 | Lecture: Normalising RNA-Seq data - Mar Gonzalez Porta (EBI) |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 11:15 | Lecture: Estimating expression with RNA-Seq - Mar Gonzalez Porta (EBI) |
| 11:15 - 12:00 | Practical: Estimating expression over genes and exonswith simple count - Mar Gonzalez Porta (EBI) |
| 12:00 - 13:00 | Lunch |
| 13:00 - 14:00 | Practical: Estimating expression over genes and exons with simple counts (cont.) - Mar Gonzalez-Porta (EBI) |
| 14:00 - 15:00 | Lecture: Differential expression analysis in RNA-seq data - Peter ‘t Hoen (LUMC) |
| 15:00 - 15:15 | Coffee Break |
| 15:15 - 17:30 | Practical: Differential expression analysis in RNA-seq data - Peter ‘t Hoen (LUMC) |
| Day 3 - Thursday 06 December 2012 | |
| 09:00 - 10:00 | Lecture: eQTL analysis - Tuuli Lappalainen (UNIGE) |
| 10:00 - 10:15 | Coffee Break |
| 10:15 - 11:30 | Practical: eQTL analysis - Tuuli Lappalainen (UNIGE) |
| 11:30 - 12:30 | Lecture: RNA-seq of HapMap cell lines - Tuuli Lappalainen (UNIGE) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Lecture: miRNA-seq analysis - Anton Enright (EBI) |
| 14:30 - 15:30 | Lecture Archiving RNA-seq data - Natalja Kurbatova (EBI) |
| 15:30 - 17:45 | Coffee Break |
| 15:45 - 17:00 | Q&A - (All) |
This event is co-sponsored by ENGAGE/GEUVADIS.
The registration fee for this event is £150.00, which includes:
* Accommodation and Breakfast for 3 nights at Hinxton Hall, The Wellcome Trust Genome Campus, Hinxton - (Check in 03 December 2012, check out 06 December 2012)
* Refreshments and lunch during the course
* Course Dinner on Tuesday evening at St John's College, Cambridge
* Course materials
* Use of EBI IT Training Room computer during the 3 day course
PLEASE NOTE: This event is now full.
All delegates will need to arrange their own travel to and from the course.