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建模碎片数量可以改善单细胞ATAC-seq分析

Laura D Martens^1,2,3, David S Fischer^2,4, Vicente A Yépez¹

¹School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.

|December 4, 2023

概括

单细胞ATAC测序数据的二元化是不必要的,也不会改善分析. 模拟碎片计数,而不是读数,保留了关键的定量监管信息,以获得更好的洞察力.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

单细胞ATAC测序 (scATAC-seq) 被广泛用于研究染色质可访问性.
监管区域通常由二元化数据 (开放/关闭的染色质) 表示.
二元化简化了数据,但可能会丢失定量信息.

研究的目的:

调查二元化在scATAC-seq数据分析中的必要性和影响.
确定替代数据建模方法是否提供了改进.
为了突出scATAC-seq.中的定量信息的重要性.

主要方法:

比较二进制与非二进制的scATAC-seq数据.
使用碎片计数与读数对数据建模的评估.
评估分析结果,包括合适度,聚类,细胞类型识别和批量集成.

主要成果:

二元化并没有提高适合性,聚类,细胞类型识别或批量集成的良性.
建模碎片计数,而不是读数,保留了定量监管信息.
阅读计数被发现对建模而言比碎片计数更不具信息性.

结论:

二元化是scATAC-seq分析中的一个不必要的步骤.
建议直接建模碎片数量,以保存定量监管信息.
这种方法可以更好地了解单细胞层面上的染色质可访问性.

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