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Analysis of DNA methylation using sequencing

 

Description

This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq (Bisulfite-Sequencing) data, common pitfalls and complications.  

It will also include exploratory analysis of methylation data, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome.  Finally the course will look at statistical methods to predict differential methylation.

The course will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages.

Trainers

Simon Andrews, Babraham Institute

Felix Krueger, Babraham Institute

 

Audience and Prerequisites

Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals.

 

Syllabus, Tools and Resources

During this course you will learn about:

  • The theoretical basis for BS-Seq
  • Processing raw sequencing data with bismark
  • Visualisation and exploration of methylation calls with SeqMonk
  • The theory of differential methylation calling
  • Differential methylation analysis with SeqMonk and the Bioconductor package BS-Seq
  • Analysing hmC with ox-BS-Seq

 

Learning Objectives

After this course you should be able to:

  • Perform an analysis of methylation data all the way from raw sequencing to the selection of interesting targets
  • Understand BS-Seq theory and quality control
  • Use SeqMonk to visualise and analyse methylation data

 

Links

Book Here

Course materials

 

Time Topic
9:30-10:30  Bisulfite-Seq theory and QC
10:30-11:15 Mapping and QC practical
11:15-11:30 Coffee
11:30-12:30 Visualising and Exploring talk
12:30-13:30 Lunch
13:30-14:00 Methylation tools in SeqMonk
14:00-15:30 Visualising and Exploring practical
15:30-15:45 coffee
15:45-16:35 Differential methylation talk & practical
16:35-16:45 Introduction to other cytosine modifications and oxBS
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