Advanced RNA-Seq and ChiP-Seq Data Analysis 2016

Date:

 Monday 18 Thursday 21 April 2016

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Wednesday November 25 2015

Application deadline: 

Friday February 26 2016

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£550.00 - (Including 3 nights accommodation, breakfasts, teas/coffees, lunches and evening meals)

Registration closed

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Overview

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. 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.

Audience

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. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.

Outcomes

After this course you should be able to:

  • Understand the advantages and limitations of the high-throughput assays presented
  • Assess the quality of your datasets
  • Understand the difference between short read aligners
  • Perform alignment and peak calling of ChIP-seq datasets
  • Perform alignment and quantification of expression of RNA-seq datasets

Programme

Time Topic Trainer
Day 1 - Monday 18 April 2016
08:15 Registration  
08:30 Overview of the course Gabriella Rustici
09:15 Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R

Nicolas Delhomme

10:15 Tea & coffee break  
10:30 Lecture/Practical: Short read representation, manipulation and quality assessment Nicolas Delhomme
11:30 Lecture/Practical: Genes and Genomes Nicolas Delhomme
12:30 Lunch  
13:30 Lecture/Practical: Genes and Genomes (continued) Nicolas Delhomme
14:00 Lecture: Mapping strategies for sequence reads Ernest Turro
15:00 Tea & coffee break  
15:15 Practical Mapping Ernest Turro
17:30 Q&A Session  
19:30 Dinner at the Red Lion Pub, Hinxton  
Day 2 - Tuesday 19 April 2016
09:00 Lecture: Representing and manipulating alignments Nicolas Delhomme
09:45 Practical: Representing and manipulating alignments Nicolas Delhomme
10:30 Tea & coffee break  
10:45 Practical: Representing and manipulating alignments Nicolas Delhomme
12:30 Lunch  
13:30 Lecture: Estimating expression over genes and exons Nicolas Delhomme
14:30 Practical: Estimating expression over genes and exons Nicolas Delhomme
15:30 Tea & coffee break  
15:45 Practical: Discovering novel transcribed regions Nicolas Delhomme
16:30 Working without a reference genome  Nicolas Delhomme
17:30 Q&A session Nicolas Delhomme
19:30 Dinner at Hinxton Hall  
Day 3 - Wednesday 20 April 2016
09:00 Lecture: Normalizing RNA-seq data Bori Mifsud & Federico Agostini
10:00 Lecture: Differential expression Bori Mifsud & Federico Agostini
11:00 Tea & coffee break  
11:15 Lecture: Multiple testing Bori Mifsud & Federico Agostini
12:30 Lunch  
13:30 Practical: Differential expression with RNA seq Bori Mifsud & Federico Agostini
15:30 Tea & coffee break  
15:45 Practical: Differential expression with RNA seq (cont.) Bori Mifsud & Federico Agostini
17:30 Q&A session  
17:45 Lecture: Single Cell sequencing John Marioni
19:30 Dinner at Hinxton Hall  
Day 4 - Thursday 21 April 2016
09:00 Lecture: Introduction to ChIP-Seq data and analysis Bori Mifsud & Federico Agostini
10:00 Lecture: Peak-callers Bori Mifsud & Federico Agostini
10:30 Tea & coffee break  
10:45 Practical: Peak-callers Bori Mifsud & Federico Agostini
12:30 Lunch  
13:30 Practical: ChIP-Seq data analysis with Bioconductor Bori Mifsud & Federico Agostini
14:30 Tea & coffee break  
14:45 Practical: ChIP-Seq data analysis with Bioconductor Bori Mifsud & Federico Agostini
16:00 Course feedback and wrap up, and delegates to depart  
16:20 Coach to Cambridge train station