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