EMBO Practical Course on Analysis of High-Throughput Sequencing Data 2015

Date:

 Monday 19 Saturday 24 October 2015

Venue: 

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

Application opens: 

Thursday June 18 2015

Application deadline: 

Friday August 14 2015

Contact: 

Johanna Langrish

Registration fee: 

Academic - £290; Industry - £715

Registration closed

Find other similar courses »

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 High-throughput sequencing 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 sequencing 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
  • Small non-coding RNA analysis: R, Reaper

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
  • Compare and apply appropriate short read aligners
  • Perform alignment and peak calling of ChIP-seq datasets
  • Perform alignment and quantification of expression for both small ncRNA and RNA-seq datasets
  • Understand the challenges of single cell sequencing analysis

Programme

Time Topic Trainer
Day 1 - Monday 19 October 2015
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, with examples from R Martin Morgan
10:15 - 10:30 Tea/coffee break  
10:30 - 11:30 Lecture/Practical: Short read representation, manipulation and quality assessment Martin Morgan
11:30 - 12:30 Lecture/Practical: Genes and Genomes Martin Morgan
12:30 - 13:30 Lunch  
13:30 - 14:00 Lecture/Practical: Genes and Genomes (continued) Martin Morgan
14:00 - 15:00 Lecture: Mapping strategies for sequence reads Ernest Turro
15:00 - 15:15 Tea/coffee break  
15:15 - 17:45 Practical: Mapping Ernest Turro
17:45 - 18:00 Q&A Session
19:00 Dinner - Wellcome Trust Genome Campus  
Day 2 - Tuesday 20 October 2015
09:00 - 09:45 Lecture: Representing and manipulating alignments Bastian Schiffthaler
09:45 - 10:30 Practical: Representing and manipulating alignments Bastian Schiffthaler
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Representing and manipulating alignments Bastian Schiffthaler
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: Estimating expression over genes and exons Bastian Schiffthaler
14:30 - 15:30 Practical: Estimating expression over genes and exons Bastian Schiffthaler
15:30 - 15:45 Tea/coffee break  
15:45 - 16:30 Practical: Discovering novel transcribed regions Bastian Schiffthaler
16:30 - 17:30 Working without a reference genome Bastian Schiffthaler
17:30 - 17:45 Q&A Session   
19:00 Dinner - Red Lion, Hinxton  
Day 3 - Wednesday 21 October 2015
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 - 15:30 Practical: Differential expression with RNA seq Wolfgang Huber
15:30 - 15:45 Tea/coffee break  
15:45 - 17:30 Practical: Differential expression with RNA seq Wolfgang Huber
17:30 - 17:45 Q&A Session  
19:00 Dinner - Red Lion Hinxton  
Day 4 - Thursday 22 October 2015
09:00 - 10:00 Lecture: Small non-coding RNA Analysis Anton Enright
10:00 - 10:15 Tea/coffee break  
10:15 - 12:30 Practical: Small non-coding RNA Analysis Enright's Lab
12:30 - 13:30 Lunch  
13:30 - 14:30 Practical: Small non-coding RNA Analysis Enright's Lab
14:30 - 15:00 Q&A session  
15:00 - 18:00 Poster Session I  
18:00 Coach depart WTCC to Cambridge  
19:30 Dinner - Jesus College, Cambridge  
Day 5 - Friday 23 October 2015
09:00 - 10:00 Lecture: Introduction to ChIP-Seq data and analysis Alessandra Vigilante & Kathi Zarnack
10:00 - 10:30 Lecture: Peak-callers Alessandra Vigilante & Kathi Zarnack
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Peak-callers Alessandra Vigilante & Kathi Zarnack
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: ChIP-Seq data analysis with Bioconductor Alessandra Vigilante & Kathi Zarnack 
14:30 - 14:45 Tea/coffee break  
14:45 - 16:45 Practical: ChIP-Seq data analysis with Bioconductor Alessandra Vigilante & Kathi Zarnack
16:45 - 17:00 Q&A session  
17:00 - 19:00 Poster session II  
19:00 Dinner - Wellcome Trust Genome Campus  
Day 6 - Saturday 24 October 2015
 09:00 - 10:00 Lecture: Single cell sequencing  John Marioni
 10:00 - 10:15 Coffee break  
 10:15 - 12:30 Practical: Single cell sequencing   Marioni's group
 12:30 - 13:00 Lunch & Feedback   
 13:00 Coach leaves to take participants to Cambridge Train Station