资产:一个端到端的管道,用于定量和可视化等位基因特异性表达
Weisheng Wu1, Kerby Shedden2, Claudius Vincenz3
1BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI, 48109, USA. weishwu@umich.edu.
BMC bioinformatics
|October 22, 2025
概括
ASE工具包 (ASET) 简化了来自RNA-Seq数据的等位基特异性表达 (ASE) 分析. 这条管道提高了用于研究基因组印记和影响转录的遗传变异的可复制性和易用性.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 分子生物学分子生物学
背景情况:
- 来自RNA测序 (RNA-Seq) 数据的基因特异表达 (ASE) 分析对于理解基因组印记和影响转录的遗传变异至关重要.
- 目前的ASE分析涉及复杂的,多步骤的计算过程,在可重复性,可扩展性和用户友好性方面提出了挑战.
研究的目的:
- 介绍ASE工具包 (ASET),一个集成的端到端管道,旨在简化SNP级ASE数据生成,可视化和原始源 (PofO) 效应测试.
- 为分子和生物医学科学家提供全面和用户友好的解决方案.
主要方法:
- ASET使用模块化Nextflow管道从短读转录组测序数据进行ASE量化.
- 它包含一个用于数据可视化的R库和用于PofO测试的Julia脚本.
- 该管道包括读数质量控制,SNP耐受性对齐,等位基因和链分辨率读数计数,基因/外因子注释和污染估计.
主要成果:
- ASET成功生成了SNP级别的ASE数据,可视化了结果,并进行了PoFO测试.
- 该工具包解决了复杂的ASE分析的可重现性和易用性方面的挑战.
结论:
- ASET提供了一个完整的,集成的解决方案,用于识别和解释来自RNA-Seq数据的ASE模式.
- 该工具包使科学家能够有效地研究基因组印记和转录相关的遗传变异.
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