This article introduces BEDTools, a versatile software package for analyzing high-throughput genomic datasets. It covers the installation and basic usage of BEDTools, including commands for finding intersections between genome interval files, measuring coverage in whole-genome and targeted DNA sequencing experiments, and assessing transcription factor occupancy at transcription start sites. The article also demonstrates how to use BEDTools to compare intervals among multiple datasets, such as Dnase I hypersensitivity sites across different human tissues. Through these examples, the author illustrates the power of combining simple BEDTools operations to create complex pipelines for addressing specific biological questions.This article introduces BEDTools, a versatile software package for analyzing high-throughput genomic datasets. It covers the installation and basic usage of BEDTools, including commands for finding intersections between genome interval files, measuring coverage in whole-genome and targeted DNA sequencing experiments, and assessing transcription factor occupancy at transcription start sites. The article also demonstrates how to use BEDTools to compare intervals among multiple datasets, such as Dnase I hypersensitivity sites across different human tissues. Through these examples, the author illustrates the power of combining simple BEDTools operations to create complex pipelines for addressing specific biological questions.