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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
Elnaz Abdollahzadeh1, Ali Mortazavi2
1Department of Developmental and Cell Biology, UC Irvine, Irvine, CA 92697, United States.
Bioinformatics (Oxford, England)
|March 2, 2026
概括
狗狗是一个新的管道,自动化牛津纳米孔测序数据分析RNA和DNA修改. 它确保直接RNA,cDNA和基因组DNA测序的可复制结果,使得全面的转录基因和表观基因洞察力.
科学领域:
- 基因组学和表观基因组学
- 计算生物学 计算生物学
- 分子生物学分子生物学
背景情况:
- 牛津纳米孔 (ONT) 测序可以直接检测RNA和DNA的修饰.
- 在ONT基础调用和分析工具的快速更新给可重复性研究带来了挑战.
- 需要标准化的计算管道来分析ONT数据.
研究的目的:
- 开发Dogme,这是一个自动化管道,用于从ONT测序数据中进行基础调用,对齐,修改检测和转录量化.
- 支持直接RNA (dRNA),互补DNA (cDNA) 和基因组DNA (gDNA) 测序数据.
- 为了方便检测各种RNA修饰 (例如m6A,m5C, inosine, pseudouridine,Nm) 和DNA甲基化.
主要方法:
- 在Nextflow中实现了Dogme,集成了像Dorado这样的基础调用工具,用于映射的minimap2和用于修改分析的modkit.
- 该管道自动化了ONT POD5文件的重新处理.
- LR-Kallisto用于对dRNA和cDNA数据的转录量化.
主要成果:
- 应用Dogme对小鼠C2C12核细胞直接RNA测序发现了许多修饰位 (例如96,603m6A,43,476m5C).
- 管道展示了可复制的修饰配置文件和跨生物复制品的转录表达水平.
- 结果突出了Dogme在综合长时间读取的转录组和表观组分析中的实用性.
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.
- 该管道简化了复杂的分析,使得人们能够更深入地了解RNA和DNA的修改.
- 狗狗是免费的,促进了表观基因组研究的标准化和可访问性.
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