DNA Methylation: Bisulfite Sequencing Workflow

Since its first use in 1992, bisulfite (BS) sequencing of DNA has become the gold standard for analysis of DNA methylation due to the potential whole-genome coverage and single-base resolution. A best-practices pipeline for the mapping and quantification of bisulfite converted reads has been developed by nf-core (see methylseq Links to an external site.). On Thursday, the use of this and other pipelines through nf-core will be extensively demonstrated. Therefore, in this tutorial we will focus on the downstream analysis, i.e. the part of the analysis after running for example nf-core methylseq. During this tutorial, you will learn how to use the methylKit R package to perform a basic bisulfite sequencing data analysis: loading data, basic quality control and filtering, data exploration and differential methylation at the CpG and regional level.

The most up-to-date version of the tutorial can be found here Links to an external site..