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

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
   • Supertracks (AKA Folders or Containers)
   • Composite Tracks
     • Subgroups
     • Views
   • Aggregate or Overlay Tracks: multiWig
4. Table of Contents

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>
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>

Less frequently used item track settings
bedNameLabel <label>
exonArrowsDense <off/on>
itemImagePath <path> <suffix> itemBigImagePath <path> <suffix>
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>
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>
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

All tracks for a hub are treated as a single group within the Browser. However hub tracks can be further subdivided with into advanced hierarchical organizations. There is even an option to combine the data of multiple remote data files into a single image.

Supertrack (Folders or Containers) settings
superTrack on
parent <superTrack>
Example of a Supertrack

Composite track settings
compositeTrack on
parent <composite> [off/on]
allButtonPair on
centerLabelsDense <off/on>
dragAndDrop on
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 <transparentOverly/solidOverlay/none>
showSubtrackColorOnUi on
Example of an Aggregate track