BED Tracks

BED Tracks are tracks for discrete signals across the entire genome. The signals are grouped by units. All units can have directions (relative to the genome), overlap with one another, have multiple segments, and/or have additional values associated with them.

BED Tracks are suitable for displaying elements such as genes, variations, regulatory elements, repeats, etc.

Data Format

Currently GIVE supports importing BED files with scripts into its data source.

The description of BED file can be seen from the UCSC Genome Browser site. A brief explanation of all fields is provided here.

BED files are text files with 3-12 fields separated by spaces or tabs (consecutive whitespaces are treated as one and empty fields must be filled with a "."). Field orders are important.

The following 3 fields are required for a BED entry:

chrom - The name of the chromosome.
chromStart - The starting position (0-based) of the entry in the chromosome.
chromEnd - The ending position of the entry in the chromosome. This base should not be included in the entry.

The 9 additional optional BED fields are:

name - Defines the name of the BED entry. This label is displayed to the left of the BED entry if there is enough space, otherwise it will be shown at the left end of the graph. See Display Modes for details about whether and where this will be shown in different modes.
score - A score between 0 and 1000. This is used for compatibility purposes and is currently not used in GIVE.
strand - Defines the strand of the entry. Use "+" for positive strand, "-" for negative strand and "." for strand-less entries. (GIVE extension: 1 or 0 can also be used to indicate positive or negative strands, respectively.)
thickStart - If this entry has a thick region (for example, exons for genes), this can be used to define the starting position of such a thick region. If omitted, thickStart will be set to the same value as chromStart.
thickEnd - The ending position of the thick region.
itemRGB - An RGB value of the form R,G,B (e.g. 255,0,0). This field is currently for compatibility purposes only and will be used to indicate the color for the entry in a future update.
blockCount - The number of blocks (exons) in this entry.
blockSizes - A list of block sizes separated by comma. The number of items in this list should equal to blockCount.
blockStarts - A list of block starts separated by comma. The positions should be relative to chromStart (therefore, the first item is typically 0). The number of items in this list should equal to blockCount.

Display Modes

BED tracks can be displayed in the following modes by setting the visibility property of the track. Available settings are listed below, from the most detailed to the least:

• Full - Every entry occupies one single line. The name of entry will be shown immediately to the left of the entry if there is enough space in the graph, otherwise it will be shown in the label region to the left of the main graph area.
• Pack - All entries and names will be shown as in Full. However, if there is space to fit multiple entries without overlapping with each other, those entries will be put in the same line.
• Collapsed - If multiple overlapping entries have the same name, they will be merged into one single “large entry” with the number of entries being merged shown in brackets after the name. This is used mainly in gene annotation tracks, where multiple transcripts of the same gene can be shown as one entity.
• Notext - Same as collapsed, except that the label is no longer shown.
• Dense - All entries are drawn in the same line whether they overlap or not.
• None - This track is not shown at all.

The display modes of tracks can be changed adaptively by setting the adaptive property of the track. If adaptive is set to true, GIVE will attempt to use the display mode that can show the most detail while keeps the total number of lines not exceeding a given value (currently at 12, will be customizable in a future update).

Supported Settings

The following settings of tracks are available for BED track:

• track - The ID of the track. This value can be used in the default-track-id-list attribute in <chart-area> tags or <chart-controller> tags.
• type - The type of the track. For BED tracks this should be bed.
• shortLabel - The label that will be shown in the label region.
• longLabel - More detailed description of the track. Will be shown in a future update.
• priority - The order of the track in the browser. A smaller value means the track will be shown in a higher location.
• visibility - The display mode of the track. See Display Modes for details.
• adaptive - Whether to change the display mode of this track adaptively. See Display Modes for details.

Supported Metadata

Currently the tracks in GIVE can have properties used to store meta data of the track. The following meta data entries are used in filtering ENCODE tracks and will be expanded to support all tracks in a future update:

• cellType - The name of the cell type. For ENCODE cell type names please refer to http://genome.ucsc.edu/ENCODE/cellTypes.html
• labName - The name of the lab which contributed this data.
• dataType - The type of the data, for example, ‘ChIP-Seq peaks’.
• trackFeature - Some data types require specification of additional features, for example, the antigen for the antibody in ChIP-Seq experiments needs to be provided.