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Fri 2 Dec 2016
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Analysis of DNA Methylation using Sequencing

Fri 2 Dec 2016


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

It will also include exploratory analysis of methylation, 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.

Course materials are available here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here

Number of sessions: 1

# Date Time Venue Trainers
1 Fri 2 Dec 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Simon Andrews,  Felix Krueger
Topics covered

Bioinformatics, Data visualisation, Data handing, Epigenetics


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

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

Presentations, demonstrations and practicals


Time Topics
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
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

1 day


A number of times per year

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