05. BED format

BED is a tabs-delimited file format allows users to define how data lines of an annotation track are displayed.

If you're unfamiliar with an annotation track, they're simply the lines that are displayed on a genome browser.

UCSC Annotation Track
itemA and itemB are sample annotation tracks.

BED files can have up to 12 columns, but only three are required for the UCSC browser, Galaxy browser and bedtools. The number of columns must be consisted throughout each row of the file.

Let's look at all 12 BED fields, as explained by the UCSC Genome Browser Information section.

3 Required BED fields

The following 3 fields are required for all BED files.

chrom
Name of chromosome - chr5, chrX, chr2_random. or scaffold - scaffold10671
chromStart
Starting position of chrom.
First base starts at 0.
chromEnd
Ending position.
This value does not get displayed. For example, the first 20 bases would have chromStart value of 0 to and chromEnd value of 20.

9 Optional BED fields

These 9 BED fields are optional.

name
Name of the BED line.
score
Score between 0 and 1000. If useScore is set to 1, the score will determine the level of gray that is displayed. A higher number equates to a darker shade.
strand
Which strand - either '+' or '-'.
thickStart
The position when the feature is drawn thickly (the start codon for gene display).
thickEnd
Ending position of where the feature is drawn thickly.
itemRgb
Determines the color of the data contained in the BED line. (255,0,0) for red.
Use the Color Picker to translate a color.
blockCount
Number of blocks (exons) in the BED line.
blockSizes
Comma-separated list of block sizes.
Size of list should correspond to blockCount.
blockStarts
A comma-separated list of block starts.
Should be calculated relative to chromStart.
Size of list should correspond to blockCount.

Example custom track

UCSC Genome BED file display.
Here we can see the track annotations that are uploaded as a BED file is onto the UCSC Genome Browser.

References

BEDtools - Read the Docs

UCSC Genome Browser - BED format

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