Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing.

ABSTRACT: DNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most important methylation in mammals is 5-methylcytosine mostly occurring in the context of CpG dinucleotides. Sequencing methods such as whole-genome bisulfite sequencing successfully detect 5-methylcytosine DNA modifications. However, they suffer from the serious drawbacks of short read lengths and might introduce an amplification bias. Here we present Rockfish, a deep learning algorithm that significantly improves read-level 5-methylcytosine detection by using Nanopore sequencing. Rockfish is compared with other methods based on Nanopore sequencing on R9.4.1 and R10.4.1 datasets. There is an increase in the single-base accuracy and the F1 measure

SUBMITTER: Stanojevic D 

PROVIDER: S-EPMC11222435 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature