What is BED format?
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. Each line contains three mandatory fields - chromosome, start position, and end position - separated by white space (i.e. space or tab). The optional fourth field provides a name for the region, and additional optional fields provide further information. Full documentation of the BED format is available from UCSC.
The coordinates in a BED record are 0-based, meaning the first base on a chromosome is numbered 0. 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 "chr1:1000-2000" would be described in a BED record as "chr1 999 2000" (with the start coordinate being one smaller and the end coordinate being the same).
Can I use a different format?
GREAT only supports BED format, which is a popular standard used by the UCSC genome browser.
What is file format for the background set?
The background set, like the main input set, must be in BED format. The background must be a superset of the main input set (that is, every record in the input set must also be in the background set).