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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| BED (file format) | 2/2 | https://en.wikipedia.org/wiki/BED_(file_format) | reference | science, encyclopedia | 2026-05-05T14:01:06.535872+00:00 | kb-cron |
== Usage == The use of BED files has spread rapidly with the emergence of new sequencing techniques and the manipulation of larger and larger sequence files. The comparison of genomic sequences or even entire genomes by comparing the sequences themselves can quickly require significant computational resources and become time-consuming. Handling BED files makes this work more efficient by using coordinates to extract sequences of interest from sequencing sets or to directly compare and manipulate two sets of coordinates. To perform these tasks, various programs can be used to manipulate BED files, including but not limited to the following:
Genome browsers: from BED files allows the visualization and extraction of sequences of mammalian genomes currently sequenced (e.g. the function Manage Custom Tracks in UCSC Genome Browser). Galaxy: web-based platform. Command-line tools: BEDTools: program allowing the manipulation of coordinate sets and the extraction of sequences from a BED file. BEDOPS: a suite of tools for fast boolean operations on BED files. BedTk: a faster alternative to BEDTools for a limited and specialized sub-set of operations. covtobed: a tool to convert a BAM file into a BED coverage track.
== .genome Files == BEDtools also uses .genome files to determine chromosomal boundaries and ensure that padding operations do not extend past chromosome boundaries. Genome files are formatted as shown below, a two-column tab-separated file with one-line header.
chrom size
chr1 248956422
chr2 242193529
chr3 198295559
chr4 190214555
chr5 181538259
chr6 170805979
chr7 159345973
...
== References ==