Abstract
Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.
Highlights
Chromosome conformation capture techniques are widely used to analyse the 3D conformation of chromatin inside the nucleus across a rising number of species, tissues and experimental conditions
Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization
With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments
Summary
Chromosome conformation capture techniques are widely used to analyse the 3D conformation of chromatin inside the nucleus across a rising number of species, tissues and experimental conditions. Hi-C data processing requires tabulating hundreds of millions to billions of paired-end reads into large matrices. This poses bioinformatic challenges for efficient processing of the data and subsequent analyses. We introduce Galaxy HiCExplorer, a package that aims to make Hi-C data processing, analysis and visualization available to non-bioinformaticians. Our goal is to provide a software environment able to automate the whole workflow of HiC data analyses from raw read mapping, filtering and correction, to the computation of topological associated domains and A/B compartments, and to the visualization of contact matrices, along with various other genomic features and omics data. Galaxy HiCExplorer is easy to install, maintainable, stable and well documented. HiCExplorer is transparently developed by a community of collaborators based on best practices [10] for version control, code revisions, manual and automated testing and comprehensive documentation
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