The article introduces BEDTools, a versatile software package for genome feature analysis. It describes how to use BEDTools for exploring high-throughput genomics datasets, focusing on common genomic analyses and demonstrating how simple BEDTools operations can be combined to create custom pipelines. BEDTools is designed for genome arithmetic tasks, such as finding overlapping intervals, calculating coverage, and comparing genomic datasets. The article provides detailed protocols for installing and using BEDTools, including examples of how to analyze genomic intervals, measure coverage in whole-genome sequencing experiments, identify regions with high or low coverage, measure coverage in targeted sequencing experiments, and compare intervals across multiple datasets. It also includes practical examples and commands for using BEDTools in various genomics analyses, such as identifying CpG islands overlapping exons, measuring sequence coverage, and visualizing transcription factor occupancy at transcription start sites. The article emphasizes the importance of understanding genome arithmetic and the flexibility of BEDTools in addressing complex genomic questions.The article introduces BEDTools, a versatile software package for genome feature analysis. It describes how to use BEDTools for exploring high-throughput genomics datasets, focusing on common genomic analyses and demonstrating how simple BEDTools operations can be combined to create custom pipelines. BEDTools is designed for genome arithmetic tasks, such as finding overlapping intervals, calculating coverage, and comparing genomic datasets. The article provides detailed protocols for installing and using BEDTools, including examples of how to analyze genomic intervals, measure coverage in whole-genome sequencing experiments, identify regions with high or low coverage, measure coverage in targeted sequencing experiments, and compare intervals across multiple datasets. It also includes practical examples and commands for using BEDTools in various genomics analyses, such as identifying CpG islands overlapping exons, measuring sequence coverage, and visualizing transcription factor occupancy at transcription start sites. The article emphasizes the importance of understanding genome arithmetic and the flexibility of BEDTools in addressing complex genomic questions.