The UCSC genome browser can load and generate a number of different file types. Their website has a good description of the formats, but we can add a few comments here.
BED Files
- BED files are the standard method for delivering locations of 'small' sets of feature, e.g., 40,000 transcription factror binding sites.
- The files do not contain any sequence information.
- BED file can be uploaded to UCSC and many other genome browsers to view results
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