Quantitative detection of DNA methylation from nanopore sequencing data without raw signals.

ABSTRACT:

Background

Nanopore sequencing has revolutionized the field of epigenomics by enabling direct detection of DNA methylation without additional sample preprocessing such as bisulfite treatment. It is theoretically possible to reutilize any nanopore sequencing data to construct epigenomes. However, reutilizing the data in practice is challenging with existing methods because they rely on raw signals from nanopore sequencing, which are absent in more than 98% of public nanopore sequencing data. Moreover, storing raw signals for large-scale sequencing projects is impractical due to their enormous file sizes.

Findings

To overcome these limitations, we propose a novel method, NanoFreeLunch, which can quantitatively detect DNA methylation without the need for raw signals by modeling

SUBMITTER: Feng Z 

PROVIDER: S-EPMC12576052 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature