ATACseqQC：一个用于评估 ATAC-seq 数据的基于 Bioconductor 的序列后质量评估工具包。
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
机构信息
Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
出版信息
BMC Genomics. 2018 Mar 1;19(1):169. doi: 10.1186/s12864-018-4559-3.
BACKGROUND
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets.
RESULTS
We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset.
CONCLUSIONS
This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .
背景
ATAC-seq（使用测序进行转座酶可及染色质分析）是一种最近开发的用于全基因组分析染色质可及性的技术。与用于检测染色质可及性的早期方法相比，ATAC-seq 更快、更容易执行，不需要交联，具有更高的信噪比，并且可以在少量细胞上进行。然而，为了确保 ATAC-seq 实验的成功，包括湿实验室质量控制和计算机质量评估在内的逐步质量保证过程是必不可少的。虽然已经开发或采用了几种工具来评估读取质量、识别来自 ATAC-seq 数据的核小体占有率和可及区域，但没有一种工具提供了用于预处理和对齐的 ATAC-seq 数据集质量评估的综合功能集。
结果
我们开发了一个 Bioconductor 包 ATACseqQC，用于轻松生成各种诊断图，以帮助研究人员快速评估其 ATAC-seq 数据的质量。此外，该软件包还包含用于预处理对齐的 ATAC-seq 数据以进行后续峰调用的功能。在这里，我们使用来自四个研究的 25 个公开的可用 ATAC-seq 数据集演示了我们软件包的实用性。我们还提供了理想的 ATAC-seq 数据集的诊断图应该是什么样子的指南。
结论
这个软件包已成功用于处理和评估多个内部和公共的 ATAC-seq 数据集。该软件包生成的诊断图将有助于 ATAC-seq 数据的质量评估，并帮助研究人员评估自己的 ATAC-seq 实验，以及从 GEO 等公共存储库中选择高质量的 ATAC-seq 数据集，以避免从低质量的 ATAC-seq 实验中生成假设或得出结论。该软件、源代码和文档可作为 Bioconductor 软件包在 https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html 上免费获得。
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