Advanced RNA-Seq and ChiP-Seq Data Analysis Course 2013
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 familiarise 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 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. 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 and ChIP-Seq experiments.
Topics will include: alignment, data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.
| Time | Topic |
|---|---|
| Day 1 - Monday, June 3 - Alignment - Materials | |
| 08:30- 09:00 | Shuttle bus from accommodation to EBI |
| 09:00 - 09:30 | Registration, welcome and introduction (Emma Hastings) |
| 09:30 - 10:30 | Lecture: Understanding the high-throughput sequencing data analysis workflow (Myrto Kostadima) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 11:00 | Introduction to Unix |
| 11-00 - 12:30 | Practical - Quality assessment and sequence manipulation (Myrto Kostadima) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Lecture - Mapping strategies for sequence reads (Ernest Turro) |
| 14:30 - 14:45 | Tea/coffee break |
| 14:45 - 17.00 | Practical - Mapping strategies for sequence reads (Ernest Turro) |
| 17:30 | Evening meal on site |
| 19:00 | Shuttle bus back to accommodation |
| Day 2 - Tuesday, June 4 - Sequence Manipulation and Basic Statistics - Materials | |
| 08:30 | Shuttle bus from accommodation to EBI |
| 09:00 - 10:15 | Lecture - Statistical concepts and methodologies for data analyses (John Marioni) |
| 10:15 - 10:30 | Tea/coffee break |
| 10:30 - 11:30 | Lecture - Statistical concepts and methodologies for data analyses (John Marioni) |
| 11:30 - 12:30 | Lecture: Expression estimation with RNA-seq (Ernest Turro) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:15 | Lecture: Normalising RNA-seq data (Mar Gonzalez-Porta) |
| 14:15 - 14:30 | Introduction to the software / R packages (Mar Gonzalez-Porta & Ernest Turro) |
| 14:30 - 15:15 | Practical |
| 15:15 - 15:30 | Tea/coffee break |
| 15:30 - 17:00 | Practical (Mar Gonzalez-Porta & Ernest Turro) |
| 17:30 | Evening meal on site |
| 19:00 | Shuttle bus to accommodation |
| Day 3 - Wednesday, June 5 - RNA-Seq - Materials | |
| 09:00 | Shuttle bus from accommodation to EBI |
| 09:30 - 10:30 | Lecture: Transcriptome assembly and differential expression analysis (Myrto Kostadima & Remco Loos) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 12:00 | Practical: Reference guided transcriptome assembly (Myrto Kostadima & Remco Loos) |
| 12:00 - 13:00 | Lunch |
| 13:00 - 15:15 | Practical: Differential expression analysis (Myrto Kostadima & Remco Loos) |
| 15:15 - 15:30 | Tea/coffee break |
| 15:30 - 16:30 | Lecture/Practical: Downstream analysis (Myrto Kostadima & Remco Loos) |
| 16:30 - 17:30 | Lecture: Archiving RNA-Seq data (Emma Hastings) |
| 17:30 | Shuttle bus back to accommodation |
| 18:45 | Coach pick-up from accommodation to Cambridge |
| 19:30 - 22:00 | Dinner at Downing College Cambridge, coach return to accommodation |
| Day 4 - Thursday, June 6 - ChIP-Seq | |
| 08:30 | Shuttle bus from accommodation to EBI |
| 09:00 - 09:45 | Lecture: Why ChIP? (Rory Stark) - Materials |
| 09:45 - 10:30 | Lecture: ChIP-Seq data analysis overview (Bori Gerle Materials & Kathi Zarnack Materials) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 12:30 | Practical: ChIP-Seq (Bori Gerle & Kathi Zarnack) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Lecture: Differential analysis of ChIP-Seq data (Rory Stark) |
| 14:30 - 14:45 | Tea/coffee break |
| 14:45 - 17:00 | Practical: Differential analysis of ChIP-Seq data with DiffBind (Rory Stark) |
| 17:15 | Farewell and departures back to accommodation |
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 5th April 2013 (12:00 midday GMT). There will be a maximum of 40 participants on this course. Successful applicants will be notified by 17th April 2013 and will then be asked to confirm their place on the course by re-registering and paying the course fee which will be confirmed at that time.
Academic Registration fee £660
Registration includes the following:
* Use of EBI IT Training Room during the 4 day course
Registration now closed for this event
This course will take place in the EMBL-EBI IT Training room which has 40 computers set up with the relevant disk images required for this course.