scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

Abstract

<jats:title>Abstract</jats:title><jats:p>Single cell chromatin accessibility sequencing (scCAS) has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. The development of several experimental protocols has led to a rapid accumulation of scCAS data. In contrast, there is a lack of open-source software tools for comprehensive processing, analysis and visualization of scCAS data generated using all existing experimental protocols. Here we present scATAC-pro for quality assessment, analysis and visualization of scCAS data. scATAC-pro provides flexible choice of methods for different data processing and analytical tasks, with carefully curated default parameters. A range of quality control metrics are computed for several key steps of the experimental protocol. scATAC-pro generates summary reports for both quality assessment and downstream analysis. It also provides additional utility functions for generating input files for various types of downstream analyses and data visualization. With the rapid accumulation of scCAS data, scATAC-pro will facilitate studies of epigenomic heterogeneity in healthy and diseased tissues.</jats:p>

Single-Cell RNA Sequencing Approaches for Tracing T Cell Development

“…Single-cell assay for transposase-accessible chromatin using sequencing (ATAC-seq) uses a hyperactive Tn5 transposase that accesses open chromatin regions and fragments the DNA. The presence of an accessible site corresponds to an active regulatory region of chromatin (70,71). Importantly, ATAC-seq information can be linked to transcriptional information.…”

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

“…The scATAC-pro software is freely available under the MIT license. Source code has been deposited at the GitHub repository (https://github.com/tanlabcode/scATAC-pro) [48] and Zenodo with the access code DOI: https://doi.org/10. 5281/zenodo.3696036 [49].…”

“…Source code has been deposited at the GitHub repository (https://github.com/tanlabcode/scATAC-pro) [48] and Zenodo with the access code DOI: https://doi.org/10. 5281/zenodo.3696036 [49]. To improve the portability of the software, we also provide a docker version of the software at https://hub.docker.com/r/wbaopaul/scatac-pro.…”

“…Accession numbers for third party data used in this study include GSE74912, GSE111586, and GSE96769. Additional simulated data sets and analysis code are described in this published article and deposited at the GitHub repository (https://github.com/tanlabcode/scATAC-pro_paper) [50] and Zenodo with the access code DOI: https://doi.org/10. 5281/zenodo.3732194 [51].…”