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.
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
|
compositeTrack on |
parent <composite> [off/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. |