Reduced Representation Bisulfite sequencing (RRBS) is a popular technique for measuring methylation levels across genome. Although it does not have the full genome coverage, it covers many important regions for methylation. Below, I shared a tutorial and slides on how to do basic RRBS analysis using R and methylKit package. The same methods can also be used on the aligned reads obtained from a target-capture protocol such as Agilent SureSelect Methyl-Seq.
The tutorial includes sections such as clustering samples and doing differential methylation analysis, and some R basics.
The tutorial is here:
The tutorial slides are below:
The slides are also downloadable from here: