EMBO Practical Course: Analysis of High-Throughput Sequencing Data
The application system requires cookies, and the limited processing of your personal data in order to function. By applying to this course you are agreeing to this as outlined in our Privacy Notice and Terms of Use
Date:
Monday 29 October 2012Application opens:
Friday 01 June 2012Application deadline:
Friday 24 August 2012Contact:
Alison BarkerRegistration 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 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 (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.
What will it cover?
The course covers data analysis of RNA-Seq and ChIP-Seq experiments.
Topics will include: short read alignment using Bowtie/BWA; data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.
Programme
| Time | Topic |
|---|---|
| Sun 28 Oct - Arrive at Wellcome Trust Conference Centre (accommodation will be here) | |
| Day 1 - Monday 29 October | |
| 08:30 - 09:00 | Registration, welcome and introduction (Gabriella Rustici) |
| 09:00 - 09:30 | Understanding the high-throughput sequencing data analysis workflow (Nicolas Delhomme) |
| 09:30 - 10:00 | Introduction to R & Bioconductor (Martin Morgan) |
| 10:00 - 10:30 | Practical: Up to speed with R (Martin Morgan) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 12:30 | Lecture/practical: Short read representation, manipulation and assessment (Martin Morgan) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Mapping strategies for sequence reads (Ernest Turro) |
| 14:30 - 15:30 | Practical: Mapping (Ernest Turro) |
| 15:30 - 15:45 | Tea/coffee break |
| 15:45 - 17:00 | Lecture: Mapping (Ernest Turro) |
| 17:00 - 17:30 | Q&A session |
| 18:30 | Dinner at the Wellcome Trust Conference Centre |
| Day 2 - Tuesday 30 October | |
| 09:00 - 10:30 | Lecture/practical: Representing and manipulating alignments (N. Delhomme/M. Morgan) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 12:30 | Lecture/practical: Annotation of genes and genomes (N. Delhomme/M. Morgan) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:15 | Lecture/practical: Estimating expression over genes and exons with simple counts (N. Delhomme/M. Morgan) |
| 15:15 - 15:30 | Tea/coffee break |
| 15:30 - 17:00 | Lecture/practical: Manipulating SNPs and Indels (N. Delhomme/M. Morgan) |
| 17:00 - 17:30 | Q&A session |
| 18:30 | Dinner at the Wellcome Trust Conference Centre |
| Day 3 - Wednesday 31 October | |
| 09:00 - 10:30 | Lecture/practical: Statistical concepts and methodologies for data analyses (Benilton Carvalho) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 11:30 | Lecture/practical: Statistical concepts and methodologies for data analyses (Benilton Carvalho) |
| 11:30 - 12:30 | Lecture: Normalising RNA-seq data (Ernest Turro) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:30 | Lecture: Haplotype and isoform level expression estimation (Ernest Turro) |
| 15:30 - 15:45 | Tea/coffee break |
| 15:45 - 17:00 | Practical: Haplotype and isoform level expression analysis practical (Ernest Turro) |
| 17:00 - 17:30 | Q&A session |
| 18:30 | Dinner at the Wellcome Trust Conference Centre |
| Day 4 - Thursday 1 November - Materials | |
| 09:00 - 10:00 | Lecture: Differential expression (Wolfgang Huber) |
| 10:00 - 11:00 | Lecture: Alternative exon usage (Wolfgang Huber) |
| 11:00 - 11:15 | Tea/coffee break |
| 11:15 - 12:30 | Lecture: Multiple testing (Wolfgang Huber) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:00 | Practical: Differential expression with RNA seq (Wolfgang Huber) |
| 15:00 - 15:15 | Tea/coffee break |
| 15:15 - 16:00 | Practical: Differential expression with RNA seq (Wolfgang Huber) |
| 16:00 - 16:30 | Q&A session |
| 16:30 - 18:00 | Poster session I |
| 19:30 | Dinner at Jesus College, Cambridge - Coach departs at 19:00 from the Conference Centre |
| Day 5 - Friday 2 November | |
| 09:00 - 10:00 | Lecture: Introduction to ChIP-Seq data and analysis (B. Gerle/K. Zarnack/R. Stark) |
| 10:00 - 10:30 | Practical: ChIP-Seq data analysis with Bioconductor (B. Gerle/K. Zarnack) |
| 10:30 - 10:45 | Tea/coffee break |
| 10:45 - 12:30 | Practical: ChIP-Seq data analysis with Bioconductor (B. Gerle/K. 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 - 16:30 | Practical: Differential analysis of ChIP-Seq data with DiffBind (Rory Stark) |
| 16:30 - 18:00 | Poster session II |
| 18:30 | Dinner at the Wellcome Trust Conference Centre |
| Day 6 - Saturday 3 November - Materials one, two, three, four, five, six | |
| 09:00 - 10:30 | ENA/SRA: introduction, data model and browsing (Rajesh Radhakrishnan/ Marc Rossello) |
| 10:30 - 10:45 | Tea /coffee break |
| 10-45 - 12:30 | SRA submissions and data compression (Rajesh Radhakrishnan/ Marc Rossello) |
| 12:30 | Course finish and departure |
How to apply
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.
Information on how to submit this additional information is contained in your completed application for registration. Application registration closes 24th August 2012 (12:00 midday GMT). There will be a maximum of 40 participants on this course. Successful applicants will be notified by 10 September 2012 and will then be asked to confirm their place on the course by re-registering.
Registration Fees:
This course is part funded by EMBO Practical Courses
Academic Registration fees are £350
Industry Registration fees are £1000
Please note that the course includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 6 nights (check in Sunday 28 October 2012, check out Saturday 3 November 2012), in the Wellcome Trust Conference Centre, Hinxton, Cambridge CB10 1SD
- College Dinner on Thursday 1st November at Jesus College Cambridge CB5 8BL
- Course materials
- Use of EBI IT Training Room computer during the 6 day course.
NOTE: All delegates will need to arrange their own travel to and from the course.
Any additional nights accommodation must be arranged directly with the Wellcome Trust Conference Centre.
Registration is now closed for this event
Please complete the application form through the link below. Items marked * are mandatory. Incomplete registrations will not be processed:
Application deadline
24 August 2012
Organisers
Gabriella Rustici
Trainers
Nicolas Delhomme - UPSC, Umeå, Sweden
Martin Morgan - Fred Hutchinson Cancer Research Center, Seattle
Wolfgang Huber - EMBL-EBI, UK