Training Recurrent Neural Networks for BrdU Detection with Oxford Nanopore Sequencing: Guidance and Lessons Learned.

ABSTRACT: Background/Objectives: BrdU (5'-bromo-2'-deoxyuridine), a synthetic thymidine (T) analog, is widely used to study cell proliferation and DNA synthesis. To precisely identify where and when DNA replication starts and terminates, it is essential to determine the BrdU incorporation rate and sites at a single-nucleotide resolution. Although several deep learning-based methods have been developed for detecting BrdU using Oxford nanopore sequencing data, there is a lack of accessible, easy-to-follow tutorials to guide researchers in preparing training data and implementing deep learning approaches as the nanopore sequencing technologies continue to evolve. Methods: Due to the lack of ground truth BrdU-positive data generated on the latest R10 flow cells, we prepared model training

SUBMITTER: Liu H 

PROVIDER: S-EPMC12652529 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature