Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data.

ABSTRACT: Background: With advances in next-generation sequencing technologies, the bisulfite conversion of genomic DNA followed by sequencing has become the predominant technique for quantifying genome-wide DNA methylation at single-base resolution. A large number of computational approaches are available in literature for identifying differentially methylated regions in bisulfite sequencing data, and more are being developed continuously. Results: Here, we focused on a comprehensive evaluation of commonly used differential methylation analysis methods and describe the potential strengths and limitations of each method. We found that there are large differences among methods, and no single method consistently ranked first in all benchmarking. Moreover, smoothing seemed not to improve

SUBMITTER: Piao Y 

PROVIDER: S-EPMC8345583 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature