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  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.
  1. Common trackDb settings
  2. Settings by track type – with examples
    • bigBed: Item or region tracks
    • bigWig: Signal graphing tracks
    • bam: Compressed Sequence Alignment/Map tracks
    • vcfTabix: Variant Call Format
  3. Grouping tracks into sets and hierarchies – with examples
  4. Table of Contents
  Common trackDb settings
 Common Settings
bigDataUrl <url/relativePath>

 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>
bamSkipPrintQualScore .
indelDoubleInsert <off/on>
indelQueryInsert <off/on>
indelPolyA <off/on>
minAliQual <#>
Related settings:
pairEndsByName .
showNames <on/off>

Additional settings found in the "Item or region tracks" section are also available for displaying bam tags.

Example of a bam track

 vcfTabix - Variant Call Format (indexed by tabix) track settings
type vcfTabix
bigDataUrl <url/relativePath>
Related settings:
hapClusterEnabled <true|false>
Related settings:
applyMinQual <true|false>
minFreq <F>

Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks.

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 settings
compositeTrack on
parent <composite> [off/on]
allButtonPair on
centerLabelsDense <off/on>
dragAndDrop subTracks
Example of a Composite track

 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