.bed

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BED is used for denoting annotations on genomes. BED stands for Browser Extensible Format, used by the UCSC genome browser. It is also used by Galaxy to convert different output to a similar format for comparison in a genomic context. It is a zero-based, fully-closed start and half-open end format: a nice discussion on what this means here.

BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.

The first three required BED fields are:

  1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
  2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
  3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display
of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases
numbered 0-99. 

The 9 additional optional BED fields are:

  4. name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when
the track is open to full display mode or directly to the left of the item in pack mode.
  5. score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score 
value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome 
Browser's translation of BED score values into shades of gray:
      shade
      score in range   	≤ 166 	167-277 	278-388 	389-499 	500-611 	612-722 	723-833 	834-944 	≥ 945
  6. strand - Defines the strand - either '+' or '-'.
  7. thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
  8. thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
  9. itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG 
value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple 
color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome
 Browser and your Internet browser.
 10. blockCount - The number of blocks (exons) in the BED line.
 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to 
chromStart. The number of items in this list should correspond to blockCount. 

Example

track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601