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Browser Extensible Data (BED) format is a file format used by the UCSC genome browser for defining genomic regions. It defines one genomic region (a "BED record") per line. GREAT requires each line to contain three mandatory fields - chromosome, start position, and end position for the region - separated by white space (i.e. space or tab). GREAT also accepts an optional region name as the fourth input field. Additional optional fields (5 and beyond) are ignored by GREAT for calculating enrichments but are fine to include in your input file as long as they conform to the BED format standards. All fields are passed to the UCSC genome browser in the tracks that GREAT creates. Full documentation of the BED format is available from UCSC.

Wiki MarkupThe coordinates in a BED record are both 0-based, meaning the first base on a chromosome is numbered 0. A BED interval is also half-opened half-closed. So, the coordinates in a BED record are slightly different than those used to find a region in the genome browser. The genome browser region "chr1:1-1000" would be described in a BED record as "chr1 0 1000" with the start coordinate being one smaller and the end coordinate being the same, describing the half-closed half-open interval \ [0,1000) of length 1000bp starting at base 0. UCSC discusses this discrepancy [here|http://genome.ucsc.edu/FAQ/FAQtracks#tracks1].

Example BED file contents

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