DNA Methylation Data Analysis Workshop

The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics. By the end of this workshop the participants will 1) be familiar with the sequencing method of Illumina, 2) understand how bisulfite sequencing works, 3) be aware of the mapping problem of bisulfite-treated data, 4) understand how bisulfite-treated reads are mapped to a reference genome, 5) be familiar with common data formats and standards, 6) know relevant tools for data processing, 7) automate tasks with shell scripting to create reusable data pipelines, 8) perform basic analyses (call methylated regions, perform basic downstream analyses), 9) plot and visualize results (ready-to-publish) and 10) be able to reuse all analyses.