Bedsect: An integrated web server application to perform intersection, visualization and functional annotation of genomic regions from multiple datasets

Abstract

A large number of genomic regions captured during next generation sequencing (NGS) data analyses are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such analysis, there is lack of a comprehensive web server application to perform the genomic region intersections from multiple datasets, to generate a plot for the subsets of the overlapped regions and to perform integrated functional annotation. To address this gap, we have developed a user-friendly integrated web server application i.e. Bedsect, where users can upload genomic regions from multiple datasets without any file number limitation and perform intersection analysis along with visualization of the intersection regions as UpSet and Correlation plot using integrated Shiny application. Bedsect also integrates GREAT for functional annotation, gene ontology, and biological pathways enrichment analysis from identified unique as well as intersected genomic regions. These genomic regions can be further uploaded in the UCSC genome browser for visualization of the results as custom tracks directly from the tool. Bedsect is available at http://imgsb.org/bedsect/.