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Updated: Jun 13, 2025
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教条:一个下一流管道用于重新处理纳米孔RNA和DNA修改
bioRxiv : the preprint server for biology
|June 12, 2025
概括
狗狗是一个Nextflow工作流程,自动化牛津纳米孔技术的数据处理,用于可复制RNA和DNA修饰检测和转录量化. 它使直接RNA,cDNA和基因组DNA测序数据的全面分析成为可能.
科学领域:
- 基因组学就是基因组学.
- 表观基因组学是指表观基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 牛津纳米孔技术 (ONT) 能够从未放大核酸中直接检测RNA和DNA修饰.
- 在ONT基础调用模型和计算工具的快速更新挑战了可重现的分析.
- 需要标准化和自动化的工作流程来准确检测修改和转录量化.
研究的目的:
- 开发 Dogme,一个基于 Nextflow 的工作流程,用于自动处理 ONT 数据.
- 为了使RNA和DNA修饰的可重复检测和转录量化.
- 支持直接RNA (dRNA),互补DNA (cDNA) 和基因组DNA (gDNA) 测序数据.
主要方法:
- Dogme自动化了ONT POD5文件处理,包括使用Dorado的基础调用和使用minimap2.2的读取映射.
- 集成使用modkit用于各种RNA修饰 (m6A,m5C, inosine, pseudouridine,Nm) 和DNA甲基化的修饰检测.
- 使用LR-Kallisto对dRNA和cDNA数据进行全长转录异型量化.
主要成果:
- 使用直接RNA测序,将Dogme应用于小鼠C2C12神经细胞.
- 在复制物中检测到数千个RNA修饰位 (m6A,m5C, inosine, pseudouridine,2'-O-甲基化).
- 证明了可重现的修改配置文件和转录表达水平,突出了整合性分析的实用性.
结论:
- 多格姆为分析ONT测序数据提供了强大且可重复的解决方案.
- 使用长读序列进行全面的转录基因和表观基因组研究.
- 工作流是自由可用的,促进了该领域的标准化.
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