Ryan's Blog

BED File Format

Posted in research by ryanlayer on January 14, 2010

BED format provides a flexible way to define the data lines that are displayed in an annotation track. 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.

If your data set is BED-like, but it is very large and you would like to keep it on your own server, you should use the bigBed data format.

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:

  1. 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.
  2. 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:
    score in range ≤ 166 167-277 278-388 389-499 500-611 612-722 723-833 834-944 ≥ 945
  3. strand – Defines the strand – either ‘+’ or ‘-‘.
  4. thickStart – The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
  5. thickEnd – The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
  6. 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.
  7. blockCount – The number of blocks (exons) in the BED line.
  8. blockSizes – A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
  9. 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.

See Example 3 for a demonstration of a custom track that uses a complete BED12 definition.

Example 5:
This example shows an annotation track that uses the itemRgb attribute to individually color each data line. In this track, the color scheme distinguishes between items named “Pos*” and those named “Neg*”. See the usage note in the itemRgb description above for color palette restrictions. NOTE: The track and data lines in this example have been reformated for documentation purposes. Click here for a copy of this example that can be pasted into the browser without editing.

browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2
chr7	127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0
chr7	127472363  127473530  Pos2  0  +  127472363  127473530  255,0,0
chr7	127473530  127474697  Pos3  0  +  127473530  127474697  255,0,0
chr7	127474697  127475864  Pos4  0  +  127474697  127475864  255,0,0
chr7	127475864  127477031  Neg1  0  -  127475864  127477031  0,0,255
chr7	127477031  127478198  Neg2  0  -  127477031  127478198  0,0,255
chr7	127478198  127479365  Neg3  0  -  127478198  127479365  0,0,255
chr7	127479365  127480532  Pos5  0  +  127479365  127480532  255,0,0
chr7	127480532  127481699  Neg4  0  -  127480532  127481699  0,0,255


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