This document describes how to process demultiplexed RRBS V2 sequencing data to extract the information from the spike-in controls included in the Premium RRBS Kit v2 in order to estimate the bisulfite conversion efficiency.
Sequences of the methylated and unmethylated spike-in controls, as well as the positions of the unmethylated cytosines present in the methylated spike-in control, can be downloaded from the ‘Documents’ section of the Premium RRBS Kit v2 page https://www.diagenode.com/en/p/premium-rrbs-kit-V2-x24:
