ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.
Front Genet
; 11: 618478, 2020.
Article
en En
| MEDLINE
| ID: mdl-33584814
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Idioma:
En
Revista:
Front Genet
Año:
2020
Tipo del documento:
Article
País de afiliación:
Taiwán