Advanced RNA-Seq and ChiP-Seq Data Analysis Course

Date:

 Monday 12 May 2014 Friday 15 May 2015

Venue: 

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

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£600

Registration closed

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.

Syllabus, tools and resources

During this course you will learn about:

  • High-throughput sequencing technology
  • Quality control of raw reads: FASTQC and fastx toolkit
  • Considerations on experiment design for ChIP-seq and RNA-seq
  • Read alignment to a reference genome: Bowtie and Tophat
  • File format conversion and processing
  • Peak calling: MACS, USeq and SISSR
  • Motif analysis: MEME
  • Quantification of expression and differential expression analysis and differential exon usage: R, DeSeq, DEXSeq

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 12 May 2014
08:15 - 08:30 Registration  
08:30 - 09:15 Overview of the course Gabriella Rustici
09:15 - 10:15 Lecture: Introduction to the high-throughput sequencing data analysis workflows, R and Bioconductor. Nicolas Delhomme
10:15 - 10:30 Tea/coffee break  
10:30 - 11:30 Lecture/Practical: Short read representation and manipulation Nicolas Delhomme
11:30 - 12:30 Lecture/Practical: Genes and Genomes Nicolas Delhomme
12:30 - 13:30 Lunch  
13:30 - 14:00 Lecture/Practical: Quality Assessment Nicolas Delhomme
14:00 - 15:00 Lecture: Mapping strategies for sequence reads Ernest Turro
15:00 - 15:15 Tea/coffee break  
15:15 - 17:30 Practical: Mapping Ernest Turro
17:30 - 17:45 HTS workflow recap Nicolas Delhomme
17:45 Q&A session  
19:00 Evening meal  
Day 2 - Tuesday 13 May 2014
09:00 - 09:45 Lecture: Representing and manipulating alignments   Nicolas Delhomme
10:00 - 10:15 Tea/coffee break  
10:15 - 11:30 Practical: Representing and manipulating alignments  Nicolas Delhomme
11:30 - 12:30 Lecture:  Estimating expression over genes and exons Nicolas Delhomme
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: Estimating expression over genes and exons Nicolas Delhomme
14:30 - 15:30 Practical: Recap and/or Advanced Bioconductor usage Nicolas Delhomme
15:30 - 15:45 Tea/coffee break  
15:45 - 16:30 Practical: Recap and/or Advanced Bioconductor usage Nicolas Delhomme
16:30 - 17:30 Working without a reference genome Nicolas Delhomme
17:30 Q&A session   
19:00 Evening meal  
Day 3 - Wednesday 14 May 2014
09:00 - 10:00 Lecture: Differential expression Benilton Carvalho
10:00 - 11:00 Lecture: Alternative exon usage Benilton Carvalho
11:00 - 11:15 Tea/coffee break  
11:15 - 12:30 Lecture: Multiple testing Benilton Carvalho
12:30 - 13:30 Lunch  
13:30 - 15:30 Practical: Differential expression with RNA seq Benilton Carvalho
15:30 - 15:45 Tea/coffee break  
15:45 - 17:30 Practical: Differential expression with RNA seq (continued) Benilton Carvalho
17:30 - 17:45 Q&A session   
17:45 - 18:30 Lecture: Single Cell sequencing John Marioni
19:30 Evening meal  
Day 4 - Thursday 15 May 2014
09:00 - 10:00 Lecture: Introduction to ChIP-Seq data and analysis Bori Gerle, Alessandra Vigilante & Anna Poetsch
10:00 - 10:30 Lecture: Peak-callers  
10:30 - 10:45 Tea/coffee break Bori Gerle, Alessandra Vigilante & Anna Poetsch
10:45 - 12:30 Practical: Peak-callers Bori Gerle, Alessandra Vigilante & Anna Poetsch
12:30 - 13:30 Lunch  
13:30 - 14:30 Practical: ChIP-Seq data analysis with Bioconductor Bori Gerle, Alessandra Vigilante & Anna Poetsch
14:30 - 14:45 Tea/coffee break  
14:45 - 16:00 Practical: ChIP-Seq data analysis with Bioconductor Bori Gerle, Alessandra Vigilante & Anna Poetsch
16:00 Course feedback and wrap up and delegates to depart