ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
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DOI：
10.1186/s12864-018-4559-3
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发表时间：
2018-03-01
期刊：
影响因子：
4.4
通讯作者：
Zhu LJ
中科院分区：
文献类型：
--
作者：
Ou J;Liu H;Yu J;Kelliher MA;Castilla LH;Lawson ND;Zhu LJ
ATAC-seq（转座酶可及染色质测序法）是最近发展起来的一种全基因组染色质可及性分析技术。与早期分析染色质可及性的方法相比，ATAC-seq更快，更容易执行，不需要交联，具有更高的信噪比，并且可以在小细胞数上执行。然而，为了确保ATAC-seq实验的成功，一步一步的质量保证过程，包括湿实验室质量控制和硅质量评估，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ATAC-seq数据中的核小体占用和可访问区域，但没有一种工具提供一套全面的功能来预处理和校准ATAC-seq数据集的质量评估。我们开发了一个Bioconductor软件包，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，这个包包含了预处理对齐ATAC-seq数据的功能，以备后续的峰值调用。在这里，我们使用来自四项研究的25个公开可用的ATAC-seq数据集来演示我们的软件包的实用程序。我们还提供了关于理想的ATAC-seq数据集的诊断图应该是什么样子的指南。该软件包已成功用于预处理和评估几个内部和公共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，以及从公共存储库（如GEO）中选择高质量的ATAC-seq数据集，以避免在低质量的ATAC-seq实验中产生假设或得出结论。该软件、源代码和文档可以在https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html上作为Bioconductor包免费获得。本文的在线版本（10.1186/s12864-018-4559-3）包含补充材料，授权用户可使用。
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. 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. 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. The online version of this article (10.1186/s12864-018-4559-3) contains supplementary material, which is available to authorized users.
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影响因子：
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影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
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3.7
作者：
Borgström E;Lundin S;Lundeberg J
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