Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information.

ABSTRACT:

Background

Whole genome sequencing of bisulfite converted DNA ('methylC-seq') method provides comprehensive information of DNA methylation. An important application of these whole genome methylation maps is classifying each position as a methylated versus non-methylated nucleotide. A widely used current method for this purpose, the so-called binomial method, is intuitive and straightforward, but lacks power when the sequence coverage and the genome-wide methylation level are low. These problems present a particular challenge when analyzing sparsely methylated genomes, such as those of many invertebrates and plants.

Results

We demonstrate that the number of sequence reads per position from methylC-seq data displays a large variance and can be modeled as a shifted negative bin

SUBMITTER: Huh I 

PROVIDER: S-EPMC4117951 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature