Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm

Yanqiang Li; Jiayi Chen; Yunxia Wang; Dean Li; Jiahan Li; Yang Yi; Lili Zhang; Qi Cao; Kaifu Chen

doi:10.1016/j.xpro.2025.104003

Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm

Yanqiang Li, Jiayi Chen, Yunxia Wang, Dean Li, Jiahan Li, Yang Yi, Lili Zhang, Qi Cao, Kaifu Chen

Research output: Contribution to journal › Article › peer-review

Abstract

2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2′-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for software installation, data collection, and training the machine learning model. We then detail procedures for mapping 2′-O-methylation in both rRNA and mRNA in yeast and human cells. For complete details on the use and execution of this protocol, please refer to Li et al.¹

Original language	English (US)
Article number	104003
Journal	STAR Protocols
Volume	6
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2025.104003
State	Published - Sep 19 2025

Keywords

Bioinformatics
Genomics
RNA-seq

ASJC Scopus subject areas

General Neuroscience
General Immunology and Microbiology
General Biochemistry, Genetics and Molecular Biology

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10.1016/j.xpro.2025.104003

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title = "Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm",

abstract = "2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2′-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for software installation, data collection, and training the machine learning model. We then detail procedures for mapping 2′-O-methylation in both rRNA and mRNA in yeast and human cells. For complete details on the use and execution of this protocol, please refer to Li et al.1",

keywords = "Bioinformatics, Genomics, RNA-seq",

author = "Yanqiang Li and Jiayi Chen and Yunxia Wang and Dean Li and Jiahan Li and Yang Yi and Lili Zhang and Qi Cao and Kaifu Chen",

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year = "2025",

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TY - JOUR

T1 - Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm

AU - Li, Yanqiang

AU - Chen, Jiayi

AU - Wang, Yunxia

AU - Li, Dean

AU - Li, Jiahan

AU - Yi, Yang

AU - Zhang, Lili

AU - Cao, Qi

AU - Chen, Kaifu

PY - 2025/9/19

Y1 - 2025/9/19

N2 - 2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2′-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for software installation, data collection, and training the machine learning model. We then detail procedures for mapping 2′-O-methylation in both rRNA and mRNA in yeast and human cells. For complete details on the use and execution of this protocol, please refer to Li et al.1

AB - 2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2′-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for software installation, data collection, and training the machine learning model. We then detail procedures for mapping 2′-O-methylation in both rRNA and mRNA in yeast and human cells. For complete details on the use and execution of this protocol, please refer to Li et al.1

KW - Bioinformatics

KW - Genomics

KW - RNA-seq

UR - https://www.scopus.com/pages/publications/105012123498

UR - https://www.scopus.com/inward/citedby.url?scp=105012123498&partnerID=8YFLogxK

U2 - 10.1016/j.xpro.2025.104003

DO - 10.1016/j.xpro.2025.104003

M3 - Article

C2 - 40751918

AN - SCOPUS:105012123498

SN - 2666-1667

VL - 6

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 104003

ER -

Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm

Abstract

Keywords

ASJC Scopus subject areas

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