AgIn: measuring the landscape of CpG methylation of individual repetitive elements.

ABSTRACT:

Motivation

Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications.

Results

We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes

SUBMITTER: Suzuki Y 

PROVIDER: S-EPMC5039925 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature