Assay of Transposase-Accessible Chromatin by deep sequencing (ATAC-seq) has been widely used to profile the chromatin accessibility genome-wide. For the absence of an integrated scheme for deep data mining of specific biological issues, here we present ATAC-pipe, an efficient pipeline for general analysis of chromatin accessibility data obtained from ATAC-seq experiments. ATAC-pipe captures information includes not only the quality of original data and genome-wide chromatin accessibility but also signatures of significant differential peaks, transcription factor (TF) occupancy and nucleosome positions around regulatory sites. In addition, ATAC-pipe automatically converts statistic results into intuitive plots at publication quality, such as the read length distribution, heatmaps of sample clustering and cell-type-specific regulatory elements, enriched TF occupancy with motifs footprints and TF-driven regulatory networks. ATAC-pipe provides convenient workflow for researchers to study chromatin accessibility and gene regulation. Availability https://github.com/QuKunLab/ATAC-pipe.

中文翻译：

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ATAC管：对全基因组染色质可及性的一般分析。

通过深度测序测定转座酶可及性染色质（ATAC-seq）已广泛用于在全基因组范围内分析染色质可及性。对于缺乏针对特定生物学问题的深度数据挖掘的集成方案，这里我们介绍ATAC-pipe，这是一种有效的管道，用于对从ATAC-seq实验获得的染色质可及性数据进行常规分析。ATAC管道捕获的信息不仅包括原始数据的质量和全基因组染色质的可及性，还包括显着的差异峰，转录因子（TF）占用率和调节位点周围核小体位置的特征。此外，ATAC管道会自动以发布质量将统计结果转换为直观的图表，例如读取长度分布，样本聚类的热图以及特定于细胞类型的调控元素，通过图案足迹和TF驱动的监管网络丰富了TF的占用。ATAC-pipe为研究人员研究染色质可及性和基因调控提供了便利的工作流程。可用性https://github.com/QuKunLab/ATAC-pipe。