Own server, you should use the bigBed data format. chrom - The name of the chromosome (e.g.chromStart - The starting position of the feature in the chromosome or scaffold.The first base in a chromosome is numbered 0. chromEnd - The ending position of the feature in the chromosome or scaffold.TheĬhromEnd base is not included in the display of the feature, however, The first 100 bases of chromosome 1 are defined as chrom=1, chromStart=0, chromEnd=100,Īnd span the bases numbered 0-99 in our software (not 0-100), but will represent theĬhromStart and chromEnd can be identical, creating a feature of length 0, commonly The number in position format will be represented. The BED line in the Genome Browser window when the track is open to full display mode or directly name - Defines the name of the BED line.The 9 additional optional BED fields are: For example, use chromStart=0, chromEnd=0 to represent an insertion before the #BAM FILE FORMAT COLUMNS SOFTWARE# Is set to 1 for this annotation data set, the score value will determine the level of #BAM FILE FORMAT COLUMNS FULL# Genome Browser's translation of BED score values into shades of gray: Gray in which this feature is displayed (higher numbers = darker gray). thickStart - The starting position at which the feature is drawn thickly (forĮxample, the start codon in gene displays).
When there is no thick part, thickStart and thickEndĪre usually set to the chromStart position. thickEnd - The ending position at which the feature is drawn thickly (for example.itemRgb - An RGB value of the form R,G,B (e.g.ItemRgb attribute is set to "On", this RBG value will determine the displayĬolor of the data contained in this BED line. Scheme (eight colors or less) be used with this attribute to avoid overwhelming the color NOTE: It is recommended that a simple color Resources of the Genome Browser and your Internet browser. blockCount - The number of blocks (exons) in the BED line.blockSizes - A comma-separated list of the block sizes.This list should correspond to blockCount. blockStarts - A comma-separated list of block starts.All of theīlockStart positions should be calculated relative to chromStart. Items in this list should correspond to blockCount. In BED files with block definitions, the first blockStart value must be 0, so that the firstīlock begins at chromStart. Similarly, the final blockStart position plus theįinal blockSize value must equal chromEnd.
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