ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces an increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. In our study, UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq, which helps identify an additional 50% or more of footprints. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.

中文翻译：

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具有独特分子标识符的ATAC-seq可改善定量和足迹

ATAC-seq（具有高通量测序的转座酶可及染色质测定）提供了一种有效的方法来分析无核小体的区域，并已被广泛用于识别转录因子的足迹。两种应用都依赖于高活性转座酶Tn5的插入事件的准确定量。但是，由于存在PCR扩增，因此无法使用标准ATAC-seq技术将独立产生的相同Tn5插入事件与PCR重复进行准确区分。根据映射坐标删除PCR重复项会导致对高度可访问的染色质区域的偏见增加。为克服此限制，我们通过将唯一的分子标识符（UMI）纳入标准ATAC-seq程序中，建立了UMI-ATAC-seq技术。在我们的研究中 UMI-ATAC-seq可以挽救大约20％的错误读数，这些读数被误认为是标准ATAC-seq中的PCR复制品，这有助于识别另外50％或更多的足迹。我们证明，UMI-ATAC-seq可以更准确地量化染色质的可及性，并显着提高识别转录因子足迹的敏感性。开发了一个分析管道以促进UMI-ATAC-seq的应用，并且可以在https://github.com/tzhu-bio/UMI-ATAC-seq上找到它。