Conversion efficiency of the Premium Bisulfite kit (Diagenode) was 99.0±0.035%, of the MethylEdge Bisulfite Conversion System (Promega) was 99.8±0.000%, of the EpiTect Bisulfite kit (Qiagen) was 98.4±0.013% and of the BisulFlash DNA Modification kit (Epigentek) was 97.9%.

What does bisulfite conversion do?

Bisulfite Conversion is a process in which genomic DNA is denatured (made single-stranded) and treated with sodium bisulfite, leading to deamination of unmethylated cytosines into uracils, while methylated cytosines (both 5-methylcytosine and 5-hydroxymethylcytosine) remain unchanged.

How do you calculate bisulfite conversion efficiency?

The bisulfite conversion rate of each base (non-CpG) can be calculated as T / (T + C) * 100, where T is thymine and C is cytosine read numbers on that base. Below is from the aligned (by bismark) and methylation-called (by methylKit) file of one sample (CHH context).