Abstract
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.
Highlights
Eukaryotic DNA is packaged together with histones to form nucleosomes, the basic unit of chromatin, which is important in determining the structure of the genome and the regulation of biological processes such as transcription
The regulatory information within chromatin can be uncovered through high-throughput sequencing methods for assaying chromatin accessibility, nucleosome positioning, histone modifications, and transcription factor (TF) occupancy
A comparison between GUAVA and currently available tools for ATAC-seq data analysis based on features such read mapping, peak calling, and differential analysis, etc
Summary
Eukaryotic DNA is packaged together with histones to form nucleosomes, the basic unit of chromatin, which is important in determining the structure of the genome and the regulation of biological processes such as transcription. Due to its ease of use, speed, low starting material requirement, reliability and multiplexing potential, ATAC-seq has been widely adopted and will most likely be the preferred method of choice in comparison to FAIRE-seq and DNase-seq for global chromatin accessibility analysis. Several bioinformatic tools are available for processing or analyzing ATAC-seq data including, NucleoATAC (Schep et al, 2015), ATACseqQC (Ou et al, 2018), ATACSeq/DNase-Seq Pipeline, and I-ATAC (Ahmed and Ucar, 2017) These tools are either command-line based or provide only partial solutions, but more importantly, most of them are complicated to use especially for biologists with little bioinformatics training, command line, and scripting experience. GUAVA package contains a complete reference manual
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