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Sodium bisulfite converts unmethylated cytosines in DNA molecules to uracils, which are read out as thymines during sequencing. However depending on the treatment time and/or experimental conditions, the conversion may not be complete, leaving certain unmethylated cytosines as C’s. The bisulfite conversion rate, defined as the rate at which unmethylated cytosines in the sample appear as T’s in the sequenced reads, is an important measure of the quality of a WGBS experiment. Estimating bisulfite conversion rate requires a priori knowledge of the methylation status on at least a portion of the cytosines in the sample.
(Song et al., 2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS One.