Biological Interpretation of Next-Generation Sequencing Data

Date:

 Monday 2 Friday 6 December 2013

Venue: 

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

Application opens: 

Monday 24 June 2013

Application deadline: 

Friday 04 October 2013

Contact: 

Frank O’Donnell

Registration closed

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Overview

The course covers analysis of NGS data. Using ChIP-Seq and RNA-Seq datasets as an example, the course will provide ideas and practical advice for the interpretation of NGS data sets in a genomic context.

Topics will include: RNA-Seq and ChIP-Seq data handling, quality assessment and visualisation; region identification and differential expression; data integration and external databases (ENCODE); statistical analysis using R/bioconductor.

 

What will I learn?

Lectures will give insight into how biological knowledge can be generated from NGS data and illustrate different ways of analysing and integrating such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of NGS data under the guidance of the lecturers and teaching assistants.

Familiarity with the technology and biological use cases of NGS is required, as is prior experience with standard RNA-Seq and/or ChIP-Seq workflows. Knowledge of R/Bioconductor and the Unix/Linux operating system are also required.

Is it right for me?

This course is aimed at advanced PhD students and post-doctoral researchers who are already applying next generation sequencing (NGS) technologies and bioinformatics methods in their research.

The aim of this course is to familiarise the participants with advanced data analysis methodologies for the interpretation and integration of data derived from different NGS applications including RNA-seq, ChIP-seq, DNA-methylation sequencing, genome-wide association studies (GWAS) and DNA variant detection.

Audience

This course is aimed at advanced PhD students and post-doctoral researchers who are already applying next generation sequencing (NGS) technologies and bioinformatics methods in their research.

Programme

Time Topic Trainer
Day 1 - Monday 2 December - Introduction to NGS analysis and ChIP-Seq
09:00 - 09:10 Welcome and introduction  
09:10 - 10:00 Lecture: Next generation sequencing overview Myrto Kostadima/ Remco Loos
10:00 - 10:15 Tea/coffee break  
10:15 - 12:30 Lecture/Practical: Introduction to ENCODE data + data retrieval practical Steven Wilder
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture & Practical: NGS quality control Myrto Kostadima/  Remco Loos
14:30 - 15:15 Lecture: Introduction to ChIP-seq Remco Loos
15:15 - 15:30 Tea/coffee break  
15:30 - 17:30 Practical: ChIP-seq analysis Remco Loos/ Steven Wilder
19:30 - Dinner @ the Wellcome Trust Conference Centre  
Day 2 - Tuesday 3 December - RNA-seq analysis
09:00 - 10:00 Lecture: Introduction to RNA-seq Myrto Kostadima/ Remco Loos
10:00 - 10:15 Tea/coffee break  
10:15 - 12:00 Practical: RNA-seq analysis - alignment Myrto Kostadima/ Remco Loos
12:00 - 13:00 Lunch  
13:00 - 15:00 Practical: RNA-seq - Transcriptome assembly Myrto Kostadima/ Remco Loos
15:00 - 15:15 Tea/coffee break  
15:15 - 17:30 Practical: RNA-seq analysis - Differential expression analysis Myrto Kostadima/ Remco Loos
19:30 - Dinner @ the Wellcome Trust Conference Centre  
Day 3 - Wednesday 4 December - Epigenetic data integration
09:00 - 09:45 Lecture: Understanding transcriptional regulation Remco Loos
09:45 - 10:00 Lecture: Introduction to datasets used for day 3 practicals Steven Wilder
10:00 - 10:15 Tea/coffee break  
10:15 - 12:00 Practical: Exploring the epigenetic landscape Remco Loos/ Steven Wilder
12:00 - 13:00 Lunch  
13:00 - 14:00 Lecture: Genome segmentation approaches Steven Wilder
14:00 - 15:00 Practical: Genome segmentation approaches Steven Wilder
15:00 - 15:15 Tea/coffee break  
15:15 - 17:30 Practical: Genome segmentation approaches (cont.) Steven Wilder
 19:30 - Dinner @ the Wellcome Trust Conference Centre  
Day 4 - Thursday 5 December - Epigenetic and gene expression data integration
09:00 - 10:00 Lecture/Practical: How to combine transcription factor binding and gene expression data I Steven Wilder
10:00 - 10:15 Tea/coffee break  
10:15 - 11:15 Lecture/Practical: How to combine transcription factor binding and gene expression data II Steven Wilder
11:15 - 12:00 Lecture: Genomic variation  David Sims
12:00 - 13:00 Lunch  
13:00 - 15:00 Practical: Genomic variation David Sims
15:00 - 15:15 Tea/coffee break  
15:15 - 16:00 Lecture: Genomic Association Andreas Heger/ Jethro Johnson
16:00 - 17:30 Practical: Genomic Association Andreas Heger/ Jethro Johnson
  Dinner @ the Wellcome Trust Conference Centre  
Day 5 - Friday 6 December - Integration across genomes
09:00 - 10:00 Lecture: Comparative genomics Andreas Heger/ Jethro Johnson
10:00 - 10:15 Tea/coffee break  
10:15 - 11:00 Practical: Comparative genomics Andreas Heger/ Jethro Johnson
11:00 - 12:00 Lecture: From genomes to networks Ian Sudbery
12:00 - 13:00 Lunch  
13:00 - 14:00 Practical: From genomes to networks Ian Sudbery
14:00 - 14:05 Wrap up and course feedback