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Collapse General Hands-on Information
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EBITrainingEBI User Training ProgrammeHands-onRNA-Seq & ChiP-Seq

Hands-on training at EBI - Advanced RNA-Seq and ChiP-Seq Data Analysis

Course Summary
Course DetailsTitle: Advanced RNA-Seq and ChiP-Seq Data Analysis
Date: 7-9 March 2011
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: Gabriella Rustici
Admin Support: Holly Foster
Registration Closes: 24 January 2011 - 12 noon (GMT)
Participation offers by: 31 January 2011




Course 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

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Time Topic
Day 1 -Monday 7 March 2011
08:45 Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections).
09:00 - 09:30 Registration
09:30 - 11:00 Lecture: Next generation sequencing theory and platforms (Harold Swerlow, WTSI)
11:00 - 11:15 Coffee Break
11:15 - 12:00 Lecture: Overview of R/Bioconductor packages for short read analysis (Nicolas Delhomme, EMBL)
12:00 - 13:00 Lunch
13:00 - 15:15 Lecture: Shortread, IRanges & Biostrings (Nicolas Delhomme, EMBL)
15:15 - 15:30 Coffee Break
15:30 - 17:30

Practical: Reading and manipulating short reads starting from SAM file, visualize alignments and coverage vectors, make quality-related plots (Nicolas Delhomme, EMBL)
Tutorial
18:00 Dinner at Red Lion, Hinxton (only for those staying at The Holiday Inn Whittlesford)
21:00 Transport - a 16 seater shuttle bus will transport you from the Red Lion, Hinxton to the The Holiday Inn (you will not all fit in it at once, it will do two collections).
Day 2 - Tuesday 8 March 2011  
08:45 Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections).
09:30 - 10:30 Lecture: Introduction to RNA-Seq data and analysis (John Marioni, EMBL-EBI)
10:30 - 10:50 Coffee Break
10:50 - 12:00 Lecture: Differential expression in count data (Thomas J. Hardcastle, Cambridge University)
12:00 - 13:00 Lunch
13:00 - 15:15

Practical: Differential expression in count data (Thomas J. Hardcastle, Cambridge University)
Tutorial
15:15 - 15:30 Coffee Break
15:30 - 17:30 ArrayExpressHTS (Angela Goncalves, EMBL-EBI)
18:00 Dinner at Red Lion, Hinxton (only for those staying at The Holiday Inn Whittlesford)
21:00 Transport - a 16 seater shuttle bus will transport you from the Red Lion, Hinxton to the The Holiday Inn (you will not all fit in it at once, it will do two collections).
Day 3 - Wednesday 9 March 2011
08:15 Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections).
09:00 - 10:00 Lecture: Introduction to ChIP-Seq data and analysis (Nicholas Luscombe, EMBL-EBI)
10:00 - 11:00 Lecture: ChIP-seq data analysis with Bioconductor (Petra Schwalie and Andre Faure, EMBL-EBI)
11:00 - 11:15 Coffee Break
11:15 - 13:00 Practical: ChIP-Seq (Petra Schwalie and Andre Faure, EMBL-EBI)
13:00 - 14:00 Lunch
14:00 - 15:00 Lecture: Genetic variation (Johan Rung, EMBL-EBI)
15:00 - 15:30 Wrap up, Q&A, feedback

Course feedback - http://www.surveymonkey.com/s/RNAseq2011

Registration and Payment

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 and research interests. Information on how to submit this additional information is contained in your completed application for registration. Application registration closes 24 January 2011. Successful applicants will be notified by 31 January 2011.

There will be a maximum of 40 participants on this course.

Registration Fees:

Registration with Accommodation Fee = £350.00
Please note that the registration with accommodation fee includes:
* All meals (breakfast, lunch, dinner and refreshment breaks)
* Accommodation for 3 nights (check in 6 March 2011, check out 9 March 2011), in the Holiday Inn, Duxford
* Transport to/from the accommodation to the EBI during the 3 days
* Course materials
* Use of EBI IT Training Room computer during the 3 day course

Registration NO Accommodation Fee = £100.00
Please note that the registration without accommodation fee includes:
* Meals at EBI (refreshments breaks and lunch)
* Course materials
* Use of EBI IT Training Room computer during the 3 day course

EBI Industry Programme Members Registration Fee = £190.00
Please note that the EBI Industry Programme Member registration fee includes:
* All meals (breakfast, lunch, dinner and refreshment breaks)
* Accommodation for 3 nights (check in 6 March 2011, check out 9 March 2011), in the Holiday Inn, Duxford
* Transport to/from the accommodation to the EBI during the 3 days
* Course materials
* Use of EBI IT Training Room computer during the 3 day course

All delegates will need to arrange their own travel to and from the course.

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Speakers


  • Andre Faure, EMBL-EBI
  • Angela Goncalves, EMBL-EBI
  • Thomas J. Hardcastle, Cambridge University
  • Nicholas Luscombe, EMBL-EBI
  • John Marioni, EMBL-EBI
  • Petra Schwalie, EMBL-EBI
  • Johan Rung, EMBL-EBI
  • Harold Swerlow, Wellcome Trust Sanger Institute
  • Nicolas Delhomme, EMBL Heidelberg
  • Gabriella Rustici, EMBL-EBI
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