Abstract
Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph.
Highlights
Chromatin is composed of nucleosomes, which each consisting of a histone octamer core wrapped by 147 bp of DNA (Tsompana and Buck, 2014), and the accessibility of chromatin can be assessed based on the nucleosome density; dense nucleosome regions are tightly packed, whereas loose nucleosome regions are more accessible
ATACgraph is able to plot the overlap between two sets of peaks from ATAC-seq and another sequencing dataset to provide the p-value of the number of overlapping peaks with a hypergeometric test
On the browser-based interface, an aligned ATAC-seq BAM file and gene annotation file are uploaded on the Galaxy platform as corresponding inputs
Summary
Chromatin is composed of nucleosomes, which each consisting of a histone octamer core wrapped by 147 bp of DNA (Tsompana and Buck, 2014), and the accessibility of chromatin can be assessed based on the nucleosome density; dense nucleosome regions (closed regions) are tightly packed, whereas loose nucleosome regions (open regions) are more accessible. Chromatin accessibility is often associated with intron retention (Reddy et al, 2012; Oka et al, 2017; Ullah et al, 2018), which plays an important role in the generation of gene product diversity Several sequencing strategies such as MNase-seq (Rizzo and Sinha, 2014), DNase-seq (Song and Crawford, 2010), FAIREseq (Giresi et al, 2007), and ATAC-seq (Buenrostro et al, 2013) have been developed for the assessment of chromatin structure. While MNaseseq identifies nucleosome-dense regions, DNase-seq and FAIREseq are used to identify open chromatin regions These techniques have hurdles that are requiring high sample quantity and processing time. Advanced users can create customized pipelines through flexible interfaces in the ATACgraph Galaxy platform
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