> For the complete documentation index, see [llms.txt](https://edu.abi.am/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://edu.abi.am/ngs-data-analysis-and-functional-genomics/file-formats-alignment-and-genomic-features/sequences-and-genomic-features-part-3-bedtools.md). # Sequences and Genomic Features Part 3: BEDtools BED (Browser Extensible Data) files are simple text files that define genomic regions of interest, such as genes, exons, or regulatory elements. They consist of columns specifying chromosome, start position, end position, and optional annotations. BED files are widely used for tasks like visualizing regions in genome browsers, performing feature-based analyses, and comparing genomic intervals. EDtools is a set of utilities often referred to as the "Swiss Army knife" of genomics. It enables a wide range of tasks, including intersecting, merging, and analyzing genomic intervals. To deepen your understanding of BEDtools and its applications in bioinformatics, watch the following videos from the Coursera course and return here to continue. * ​[Sequences and Genomic Features 9: BEDtools I](https://www.coursera.org/learn/genomic-tools/lecture/6SpUD/sequences-and-genomic-features-9-bedtools-i)​ * ​[Sequences and Genomic Features 10: BEDtools II](https://www.coursera.org/learn/genomic-tools/lecture/xcDQV/sequences-and-genomic-features-10-bedtools-ii)​ Now, read [the instructions](https://www.coursera.org/learn/genomic-tools/supplement/4zWiX/module-2-exam-instructions-important) and complete the [practice quiz](https://www.coursera.org/learn/genomic-tools/exam/c9MBd/module-2-exam). ### Materials You can use the following files, which are similar to the examples presented in the video. The **bed** files are stored in the following directory on the server: > bed/ --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://edu.abi.am/ngs-data-analysis-and-functional-genomics/file-formats-alignment-and-genomic-features/sequences-and-genomic-features-part-3-bedtools.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.