GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data.
GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data.
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DOI：
10.3389/fgene.2018.00250
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发表时间：
2018
影响因子：
3.7
通讯作者：
Cheung E
中科院分区：
文献类型：
--
作者：
Divate M;Cheung E
高通量测序法检测转座酶可降解染色质（ATAC-seq）是一种强大的基因组技术，用于开放染色质区域的全局定位和分析。然而，对于处理和分析这样的数据的用户，他们必须使用许多复杂的生物信息学工具或尝试使用当前可用的ATAC-seq分析软件，其不是非常用户友好的并且缺乏ATAC-seq结果的可视化。由于这些问题，希望自己处理和分析自己的ATAC-seq数据的生物信息学背景最低的生物学家会发现这些任务很困难，最终需要寻求生物信息学专家的帮助。此外，没有可用的工具提供完整的解决方案ATAC-seq数据分析。因此，为了使非编程研究人员能够自己分析ATAC-seq数据，我们开发了一个名为ATAC-seq数据分析和可视化图形用户界面（GUAVA）的工具。GUAVA是一个独立的软件，为用户提供从始至终的无缝解决方案，包括适配器修剪，读取映射，ATAC-seq峰的识别和差异分析，功能注释以及ATAC-seq结果的可视化。我们相信GUAVA将是一个非常有用和节省时间的工具，用于分析ATAC-seq数据，为生物学家提供最少或没有生物信息学背景。由于GUAVA还可以通过命令行操作，因此可以轻松集成到现有管道中，从而为具有计算经验的用户提供灵活性。
Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a powerful genomic technology that is used for the global mapping and analysis of open chromatin regions. However, for users to process and analyze such data they either have to use a number of complicated bioinformatic tools or attempt to use the currently available ATAC-seq analysis software, which are not very user friendly and lack visualization of the ATAC-seq results. Because of these issues, biologists with minimal bioinformatics background who wish to process and analyze their own ATAC-seq data by themselves will find these tasks difficult and ultimately will need to seek help from bioinformatics experts. Moreover, none of the available tools provide complete solution for ATAC-seq data analysis. Therefore, to enable non-programming researchers to analyze ATAC-seq data on their own, we developed a tool called Graphical User interface for the Analysis and Visualization of ATAC-seq data (GUAVA). GUAVA is a standalone software that provides users with a seamless solution from beginning to end including adapter trimming, read mapping, the identification and differential analysis of ATAC-seq peaks, functional annotation, and the visualization of ATAC-seq results. We believe GUAVA will be a highly useful and time-saving tool for analyzing ATAC-seq data for biologists with minimal or no bioinformatics background. Since GUAVA can also operate through command-line, it can easily be integrated into existing pipelines, thus providing flexibility to users with computational experience.