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  Track Database Definition

Hub Track Database Definition (v0)

How to declare Dataset Display Settings in Genome Browser Hubs

This document describes how to declare dataset display characteristics in a Genome Browser Hub through trackDb settings (please note that hosting hub files on HTTP tends to work even better than FTP). Introducing datasets for display in the Browser requires declaring the location and format of the data and defining initial display characteristics. In many cases, you may need to choose how the displayed data (aka "track") may be selected and configured. These settings are declared in a simple text file format and loaded into the Browser's "track database", or trackDb for short.

The text file format for trackDb settings follow the simple "ra" rules which establish a "record" as a set of related settings in a "stanza" delimited by blank lines. The first line of each stanza typically establishes the "key". Each line in a stanza will contain a single word "setting" name and one or more words or numbers that follow are the setting's "value". All trackDb stanzas are keyed by "track" and most will have certain common settings followed by track specific settings. Here is an example:

        track myFirstTrack
        type bigBed 3
        bigDataUrl myFirstTrack.bb
        shortLabel Example Data
        longLabel The data in this track is format "bigBed 3".    

Every hub track should have these five settings. The key of this track (myFirstTrack) is the name of the dataset and is typically the root file name. However, this is a key to the track so it must be unique within your data hub. After the "track" key, the most important setting for defining a track is the "type". This tells the Browser which format the data is in, defines how to display it, and determines which options are available for fine control of that display.

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

 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>
itemRgb on
colorByStrand <red,green,blue> <red,green,blue>
denseCoverage <maxVal>
labelOnFeature <on/off>
exonArrows <on/off>
exonNumbers <on/off>
scoreFilter <low>[:<high>]
scoreFilterLimits <low>[:<high>]
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 <#> <#>
autoScale <off/on>
maxHeightPixels <max:default:min>
viewLimits <lower:upper>
viewLimitsMax <lower:upper>
alwaysZero <off/on>
bigDataUrl <url/relativePath>
graphTypeDefault points
maxWindowToQuery <integer>
negateValues <on>
smoothingWindow <off/1-16>
transformFunc <NONE/LOG>
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 .
code class="level-full">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.

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>
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.

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 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…]
subGroup3 subGroup4 subGroup5 subGroup6 subGroup7 subGroup8 subGroup9
subGroups <gTag1=mTag1?> [gTag2= mTag2?]
dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]
filterComposite <dim[A/B/C][=one]> [dimB dimC ...]
dimensionAchecked <mTag1a> [mTag1b …]
dimensionBchecked dimensionCchecked
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

Miscellaneous Deprecated Settings

SettingFor TypesNotes
all
noInheritall
useScore bed, factorSource, bed5FloatScore, broadPeak Replaced with spectrum.