This document describes how to set dataset display characteristics in a Genome Browser Hub using trackDb settings. These settings are used to declare the location and format of a dataaset and to customize the display appearance. They are defined in a simple text file format and loaded into the Browser's "track database", or trackDb for short.
While there are over 100 supported settings (providing a high level of flexibility for track display), only 5 are required to define a track. To foster portability to other sites that display track hubs, a subset of settings are designated 'base' and this specification document is assigned a version number. All settings in this document are assigned a 'support level', shown here in the setting title color, the description, and the Table of Contents. The support levels are:
required | required settings |
base | common settings supported at other sites |
deprecated | settings that are being retired (replacement is listed in details section) |
new | new settings not yet assigend a level (may be replaced) |
full | other settings |
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.
track |
type |
shortLabel |
longLabel |
bigDataUrl <url/relativePath> |
html |
visibility |
Many settings are valid only for certain types of tracks. Many of these tracks are described below along with settings specific to their types.
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 . |
code class="level-full">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
|
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
|
superTrack on |
parent <superTrack> |
Example of a Supertrack
|
parent <composite> [off/on] |
compositeTrack on |
allButtonPair on |
centerLabelsDense <off/on> |
dragAndDrop subTracks |
Example of a Composite track
|
container multiWig |
parent <containerTrack> |
aggregate <transparentOverlay/stacked/solidOverlay/none> |
showSubtrackColorOnUi on |
Example of an Aggregate track
|
Setting | For Types | Notes |
---|---|---|
metadata
|
all | |
noInherit | all | |
useScore |
bed, factorSource, bed5FloatScore, broadPeak | Replaced with spectrum. |