Advanced RNA-Seq and ChiP-Seq Data Analysis

Date:

 Monday 24 Thursday 27 April 2017

Venue: 

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

Application opens: 

Monday November 21 2016

Application deadline: 

Friday January 20 2017

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£550

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 24 April 2017
09:00 Arrival and registration  
09:15 Overview of the course

Gabriella Rustici

09:45 Lecture: Introduction to the high-throughput sequencing data analysis workflows Nicolas Delhomme & Bastian Schiffthaler
10:45 Tea & coffee break  
11:00 Lecture: Sequence reads - formats and quality assessment Nicolas Delhomme & Bastian Schiffthaler
11:45 Practical: Quality assessment Nicolas Delhomme & Bastian Schiffthaler
13:00 Lunch  
14:00 Lecture: Mapping strategies for sequence reads Nicolas Delhomme & Bastian Schiffthaler
15:00 Practical: Mapping Nicolas Delhomme & Bastian Schiffthaler
15:30 Tea & coffee break  
15:45 Practical: Mapping Nicolas Delhomme & Bastian Schiffthaler
16:30 Lecture: Alignments - Formats and manipulation Nicolas Delhomme & Bastian Schiffthaler
17:00 Practical: Alignments - Formats and manipulation Nicolas Delhomme & Bastian Schiffthaler
18:00 Q&A Session  
19:30 Dinner at Hinxton Hall  
Day 2 - Tuesday 25 April 2017
09:00 Lecture: Annotation - Genes and Genomes  
09:45 Practical: Annotation - Genes and Genomes  
10:30 Tea & coffee break  
10:45 Lecture: Estimating expression - Genes and Transcripts Nicolas Delhomme & Bastian Schiffthaler
11:30 Practical: Estimating expression - Genes and Transcripts Nicolas Delhomme & Bastian Schiffthaler
13:00 Lunch  
14:00 Lecture: Differential expression Charlotte Soneson
15:30 Tea & coffee break  
15:45 Lecture: Differential expression + A comparison of methods for differential expression analysis of RNA-seq data Charlotte Soneson
17:30 Q&A session  
19:00 Dinner at Hinxton Hall  
Day 3 - Wednesday 26 April 2017
09:00 Practical: Differential expression with RNA seq Charlotte Soneson
11:00 Tea & coffee break  
11:15 Practical: Differential expression with RNA seq (cont.) Charlotte Soneson
12:30 Lunch  
13:30 Lecture: Downstream analysis Nicolas Delhomme & Bastian Schiffthaler
14:30 Tea & coffee break  
14:45 Practical: Downstream analysis Nicolas Delhomme & Bastian Schiffthaler
16:30 Q&A session  
18:00 Dinner at Hinxton Hall  
Day 4 - Thursday 27 April 2017
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 (cont.) Bori Mifsud & Federico Agostini
16:00 Course feedback and wrap up, and delegates to depart  
16:20 Coach to Cambridge train station