UCSC Track Database Definition

Track Database Definition

The remainder of this document is divided into the following sections and should be used as a ready reference.

Expand/close descriptions of settings in the sections below.

Common trackDb settings

Common Settings

`track`
`type`
`shortLabel`
`longLabel`
`bigDataUrl <url/relativePath>`
`visibility`
`html`

Common Optional Settings

`boxedCfg <on/off>`
`color <red,green,blue>`
`altColor <red,green,blue>`
`chromosomes <chr1,chr2,...>`
`dataVersion <str>`
`directUrl <url>`
`iframeUrl <url>`
`iframeOptions <string>`
`otherDb <otherDb>`
`pennantIcon <icon> [html [tip]]`
`priority <float>`
`url <url>` `urlLabel <label>`
`urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...`

Settings by track type

Many settings are valid only for certain types of tracks. Many of these tracks are described below along with settings specific to their types.

bigBed - Item or region track settings

`type bigBed <3-12> [+/.]`
`bigDataUrl <url/relativePath>`
`colorByStrand <red,green,blue> <red,green,blue>`
`denseCoverage <maxVal>`
`labelOnFeature <on/off>`
`exonArrows <on/off>`
`scoreFilter <low>[:<high>]` `scoreFilterLimits <low>[:<high>]`
`itemRgb on`
`maxItems <integer>`
`maxWindowToDraw <integer>`
`minGrayLevel <1-9>`
`noScoreFilter on`
`spectrum on` `scoreMax <integer>` `scoreMin <integer>`
`thickDrawItem <off/on>`
`searchIndex <str>`
`searchTrix <url/relativePath>`

Less frequently used item track settings
`bedNameLabel <label>`
`exonArrowsDense <off/on>`
`itemImagePath <path> <suffix>` `itemBigImagePath <path> <suffix>`
`linkIdInName on`
`nextExonText <str>` `prevExonText <str>`
`showTopScorers #`
Examples of item base types

bigWig - Signal graphing track settings

`type bigWig <#> <#>`
`alwaysZero <off/on>`
`autoScale <off/on>`
`bigDataUrl <url/relativePath>`
`graphTypeDefault points`
`maxHeightPixels <max:default:min>`
`maxWindowToQuery <integer>`
`negateValues <on>`
`smoothingWindow <off/1-16>`
`transformFunc <NONE/LOG>`
`viewLimits <lower:upper>` `viewLimitsMax <lower:upper>`
`windowingFunction <mean/mean+whiskers/maximum/minimum>`
`yLineMark <#>` `yLineOnOff <off/on>` `gridDefault on`
Examples of signal graphing tracks

bam - Compressed Sequence Alignment track settings

`type bam`
`bigDataUrl <url/relativePath>`
Related settings: `bamColorMode <strand/gray/tag/off>`
`bamGrayMode <aliQual/baseQual/unpaired>` `aliQualRange <min:max>` `baseQualRange <min:max>`
`bamColorTag <XX>`
`noColorTag .`
`bamSkipPrintQualScore .`
`indelDoubleInsert <off/on>` `indelQueryInsert <off/on>` `indelPolyA <off/on>`
`minAliQual <#>`
Related settings: `pairEndsByName .`
`pairSearchRange <#>`
`showNames <on/off>`
Additional settings found in the "Item or region tracks" section are also available for displaying bam tags. maxWindowToDraw,
Example of a bam track

vcfTabix - Variant Call Format (indexed by tabix) track settings

`type vcfTabix`
`bigDataUrl <url/relativePath>`
Related settings: `hapClusterEnabled <true\|false>`
`hapClusterColorBy <altOnly\|refAlt\|base>`
`hapClusterTreeAngle <triangle\|rectangle>`
`hapClusterHeight <N>`
Related settings: `applyMinQual <true\|false>`
`minQual <Q>`
`minFreq <F>`
Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks. maxWindowToDraw
Example of a VCF track

Grouping tracks into sets and hierarchies

Depending on how closely related they are, tracks can be organized into one of three hierarchical containers:

"multiWig" container: when the tracks are all in signal (wiggle or bigWig) format and it makes sense to overlay them.
Example: a set of bigWig tracks with H3K27ac signal, all on the same scale
"composite" container: when the tracks are expected to be configured together or have an internal subgrouping, like cell type or cell treatment.
Example: a set of ChIP-bigBeds in three different cell types
"superTrack" container: when the tracks share no specific configuration and you mostly want to show them together.
Example: a set of composite tracks or a mix of bigBed, bigWig and bam

Supertrack (Folders) settings

`superTrack on`
`parent <superTrack>`
Example of a Supertrack

Composite track subgroup settings

`subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]` `subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]`
`subGroups <gTag1=mTag1?> [gTag2= mTag2?]`
`dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]`
`filterComposite <dim[A/B/C][=one]> [dimB dimC ...]`
`dimension<?>checked <mTag1a> [mTag1b …]`
`sortOrder <gTag#=+/-> [gTag#=- …]`
Examples of Composite tracks with Subgroups

Composite track View settings

`subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]` `track <viewName>` `view <viewTag>`
`subGroups view=<vTag1>…` `parent <viewName> [off/on]`
`viewUi on`
`configurable <off/on>`
Example of a Composite track with Views

Aggregate or Overlay track settings

`container multiWig`
`parent <containerTrack>`
`aggregate <transparentOverlay/stacked/solidOverlay/none>`
`showSubtrackColorOnUi on`
Example of an Aggregate track