Advanced RNA-Seq and ChiP-Seq Data Analysis Course 2012
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Date:
Tuesday 1 May 2012Application deadline:
Tuesday 06 March 2012Contact:
Johanna LangrishRegistration closed
Overview
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 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.
Programme
| Time | Topic |
|---|---|
| Day 1 - Tuesday 01 May 2012 - Alignment | |
| 12:30 - 13:00 | Registration |
| 13:00 - 14:00 | Understanding the high-throughput sequencing data analysis workflow (Angela Goncalves & Mar Gonzalez-Porta) |
| 14:00 - 15:45 | Practical - (Angela Goncalves & Mar Gonzalez-Porta) |
| 15:45 - 16:00 | Coffee break |
| 16:00 - 17:15 | Lecture - Mapping strategies for sequence reads - (Ernest Turro) |
| Day 2 - Wednesday 02 May 2012 - Sequence Manipulation and Basic Statistics | |
| 09:00 - 11:00 | Lecture - Statistical concepts and methodologies for data analyses - (Benilton Carvalho) |
| 11:00 - 11:15 | Coffee Break |
| 11:15 -12:30 | Practical - Statistical concepts and methodologies for data analyses - (Benilton Carvalho) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:15 |
Lecture: (Angela Goncalves & Mar Gonzalez-Porta) |
| 14:15 - 14:45 | Lecture: Haplotype and isoform level expression estimation - (Ernest Turro) |
| 14:45 - 15:15 |
Lecture: Normalising RNA-Seq Data - (Ernest Turro) |
| 15:15 - 15:30 | Coffee Break |
| 15:30 - 17:30 | Practical: (Angela Goncalves, Mar Gonzalez-Porta & Ernest Turro) |
| Day 3 - Thursday 03 May 2012 - RNA-Seq | |
| 09:30 - 10:30 | Lecture: Introduction to RNA-Seq data and analysis - (John Marioni) |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:00 | Lecture: Differential expression in count data - (Thomas J. Hardcastle) |
| 12:00 - 13:00 | Lunch |
| 13:00 - 15:15 | Practical: Differential expression in count data - (Thomas J. Hardcastle) |
| 15:15 - 15:30 | Coffee Break |
| 15:30 - 17:30 | Lecture: Archiving RNA-Seq data (Gabriella Rustici) |
| Day 4 - Friday 04 May 2012 - ChIP-Seq | |
| 09:00 - 09:45 | Lecture: Introduction to ChIP-Seq data and analysis - (Bori Gerle & Kathi Zarnack) |
| 09:45 - 10:30 | Lecture: ChIP-Seq data analysis with Bioconductor - (Bori Gerle & Kathi Zarnack) |
| 10:30 - 10:45 | 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 | Coffee Break |
| 14:45 - 16:00 | Practical: Differential analysis of ChIP-Seq data with DiffBind - (Rory Stark) |
How to apply
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for a place on this course, they MUST submit a short CV, Research Interests and a Letter of Support. Information on how to submit this additional information is contained in your completed personal details application for registration. Application registration closes 06 March 2012 (12:00 Midday GMT). Successful applicants will be notified by 14 March 2012.
There will be a maximum of 40 participants on this course.
N.B. You will not need to pay any money at the application stage. Payment will only be required once you have been accepted onto the course.
Registration Fees:
Registration Fee = £420.00
Please note that the registration fee includes:
* All refreshments (lunch, refreshment breaks and evening meals)
* 3 nights accommodation at the Wellcome Trust Conference Centre (Arrive 01 May 2012 - Departure 04 May 2012)
* Course materials
* Use of EBI IT Training Room computer during the course
EBI Industry Programme Members Registration Fee = £200.00
Please note that the EBI Industry Programme Member registration fee includes:
* All refreshments (lunch, refreshment breaks and evening meals)
* 3 nights accommodation at the Wellcome Trust Conference Centre (Arrive 01 May 2012 - Departure 04 May 2012)
* Course materials
* Use of EBI IT Training Room computer during the course
RGISTRATION FOR THIS EVENT HAS NOW CLOSED
Please note: Accommodation has been booked at the 'Welcome Trust Conference Centre' (walking distance to the training venue). There is no seperate registration fee for registration only. Travel to and from the course is not provided.
Speakers
- Benilton Carvalho, University of Cambridge
- Bori Gerle, EMBL-EBI
- Angela Goncalves, EMBL-EBI
- Mar Gonzalez Porta, EMBL-EBI
- Thomas J. Hardcastle, Univeristy of Cambridge
- Gabriella Rustici, EMBL-EBI
- Rory Stark - CRUK
- Kathi Zarnack, EMBL-EBI
Application deadline
06 March 2012
Organisers
Gabriella Rustici
Trainers
Gabriella Rustici - EMBL-EBI, UK
Paul Flicek - EMBL-EBI, UK
Sandro Morganella - EMBL-EBI, UK
Kathi Zarnack - Buchmann Institute for Molecular Life Sciences, Frankfurt
Ewan Birney - EMBL-EBI, UK
Christoph Steinbeck - EMBL-EBI, UK
Ernest Turro - University of Cambridge
Thomas. J. Hardcastle - University of Cambridge
Henning Hermjakob - EMBL-EBI, UK