NOTE: The track and data lines in this example have been reformatted forĭocumentation purposes. Usage note in the itemRgb description above for color palette In this track, the color scheme distinguishesīetween items named "Pos*" and those named "Neg*". This example shows an annotation track that uses the itemRgb attribute to Here's an example of an annotation track, introduced by a header line, that is followed by a complete BED definition: track name=pairedReads description="Clone Paired Reads" useScore=1Ĭhr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512Ĭhr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
Similarly, the finalīlockStart position plus the final blockSize value must equal In BED files with block definitions, the first blockStart value mustīe 0, so that the first block begins at chromStart. This list should correspond to blockCount. blockStarts - A comma-separated list of block starts.Īll of the blockStart positions should be calculated relative to.The number of items in this list should correspond to blockSizes - A comma-separated list of the block.blockCount - The number of blocks (exons) in the.Overwhelming the color resources of the Genome Browser and your (eight colors or less) be used with this attribute to avoid NOTE: It is recommended that a simple color scheme This RBG value will determine the display color of the data contained If the track line itemRgb attribute is set to "On", itemRgb - An RGB value of the form R,G,B (e.g.thickEnd - The ending position at which the feature isĭrawn thickly (for example, the stop codon in gene displays).When there is no thick part, thickStart and thickEnd are Is drawn thickly (for example, the start codon in geneĭisplays). thickStart - The starting position at which the feature.strand - Defines the strand - either '+' or '-'.This table shows the Genome Browser's translation of BED score values into This feature is displayed (higher numbers = darker gray). Score value will determine the level of gray in which
UseScore attribute is set to 1 for this annotation data set, the
Window when the track is open to full display mode or directly to the This label isĭisplayed to the left of the BED line in the Genome Browser name - Defines the name of the BED line.The 9 additional optional BED fields are: For example, the first 100 bases of aĬhromosome are defined as chromStart=0, chromEnd=100, and span The chromEnd base is not included in theĭisplay of the feature. chromEnd - The ending position of the feature in theĬhromosome or scaffold.The first base in a chromosome is numbered 0. chromStart - The starting position of the feature in theĬhromosome or scaffold.chr3, chrY,Ĭhr2_random) or scaffold (e.g. chrom - The name of the chromosome (e.g.It on your own server, you should use the If your data set is BED-like, but it is very large (over 50MB) and you would like to keep Which convert lines of BED text to indexed binary files. Permissible in downstream utilities such as bedToBigBed Such annotation track header lines are not The lines of BED data following the headers. Or "track" to assist the browser in the display and interpretation of The file consist of header lines, which begin with the word "browser" Please note that only in custom tracks can the first lines of Only some variations of BED types, such as The order of the optional fields is binding: lower-numbered fields must alwaysīe populated if higher-numbered fields are used.īED information should not be mixed as explained above (BED3 should notīe mixed with BED4), rather additional column information mustīe filled for consistency, for example with a "." in some circumstances, Line must be consistent throughout any single set of data in an annotation track. Required fields and nine additional optional fields.