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.
A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe is a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.
Quantifies oxi-mC species with arbitrary covariate structures from bisulphite based sequencing data. LuxGLM was developed to improve the analysis of DNA methylation modifications, particularly for oxi-mC species. This method is applicable in analysis of genome-wide, reduced representation and targeted bisulphite sequencing data. It also provides methylation level estimates and detection of differential methylation.