Track Database Definition

        track myFirstTrack
        type bed 6
        shortLabel Example Data
        longLabel The data in this track is format "bed 6".    

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
   • bed/bigBed: Item or region tracks
   • wig/bigWig/bedGraph: Signal graphing tracks
   • genePred/bigGenePred: Gene models and predictions
   • bam/cram: Compressed Sequence Alignment/Map tracks
   • pgSnp: Personal Genome SNP tracks
   • vcfTabix: Variant Call Format
   • psl/bigPsl: Sequence alignments
   • chain/bigChain and netAlign: Paired sequence alignments
   • wigMaf/bigMaf: Multiple alignments
   • expRatio: Microarray expression data
   • snp: Short genetic variants from dbSNP
   • barChart/bigBarChart: Categorical values over a region
   • interact/bigInteract: Pairwise interactions
   • Specialize or rarely used:
     altGraphX, bedDetail, clonePos, ctgPos, downloadsOnly, encodeFiveC, factorSource, rmsk and snake.
3. Grouping tracks into sets and hierarchies – with examples
   • Predefined major track groupings
   • Supertracks (Folders)
   • Composite Tracks
     • Subgroups
     • Views
   • Aggregate or Overlay Tracks: multiWig
4. Special settings for custom tracks
5. Obscure or special cases – (aka Rejections)
6. Table of Contents

Many settings are valid only for certain types of tracks. These track types are described below along with the settings specific to their types.

bed/bigBed - Item or region track settings
type bed <3-12> [+/.] type bigBed <3-12> [+/.]
type bed5FloatScore type bedRnaElements type broadPeak type coloredExon type gvf type ld2 type narrowPeak type peptideMapping
bigDataUrl <url/relativePath>
colorByStrand <red,green,blue> <red,green,blue>
compareGenomeLinks <db[.table[.column]]=label> [db[.table[.column] =label …]
denseCoverage <maxVal>
labelOnFeature <on/off>
exonArrows <on/off>
exonNumbers <on/off>
<column>Filter <low>[:<high>] scoreFilter <low>[:<high>] pValueFilter qValueFilter signalFilter <column>FilterLimits <low>[:<high>] <column>FilterByRange <off/on>
filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]
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
bedFilter on
bedNameLabel <label>
Related settings: baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >
baseColorUseCds <given/table <table>>
baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
baseColorTickColor <lighterShade/contrastingColor>
showDiffBasesAllScales on
showDiffBasesMaxZoom <basesPerPixel>
showCdsAllScales
showCdsMaxZoom <basesPerPixel>
exonArrowsDense <off/on>
itemDetailsHtmlTable <table>
itemImagePath <path> <suffix> itemBigImagePath <path> <suffix>
linkIdInName on
mafTrack <trackName>
nextExonText <str> prevExonText <str>
scoreLabel <label>
showTopScorers #
Examples of item base types

wig,bigWig - Signal graphing track settings
type wig <low#> <high#> type bigWig <#> <#>
type bedGraph <field> minLimit <#> maxLimit<#>
alwaysZero <off/on>
autoScale <off/on>
bigDataUrl <url/relativePath>
graphTypeDefault points
maxHeightPixels <max:default:min>
maxWindowToQuery <integer>
negateValues <on>
spanList <s1>[,s2…]
smoothingWindow <off/1-16>
transformFunc <NONE/LOG>
viewLimits <lower:upper> viewLimitsMax <lower:upper>
wigColorBy <bedTable>
windowingFunction <mean/mean+whiskers/maximum/minimum>
yLineMark <#> yLineOnOff <off/on> gridDefault on
Examples of signal graphing tracks

genePred - Gene model track settings
type genePred [pepTable [mrnaTable]]
Related settings: geneClasses <cl1 cl2...>
gClass_<xxx> <red,green,blue>
itemClassTbl <table>
itemClassNameColumn <col>
itemClassClassColumn <col>
filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]
autoTranslate 0
intronGap <#bases>
defaultLinkedTables <table1>[,table2...]
idXref <idColumn> <altIdColumn>
oldToNew <tableName>
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. baseColorUseSequence, baseColorDefault, itemDetailsHtmlTable, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Examples of genePred tracks

bam/cram - Compressed Sequence Alignment track settings
type bam
bigDataUrl <url/relativePath>
bigDataIndex <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>
doWiggle on
Additional settings found in the "Item or region tracks" section are also available for displaying bam tags. baseColorUseSequence, baseColorDefault, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Example for bam track:

bigBarChart - Bar chart display of categorical variables over genomic regions
type bigBarChart
barChartBars <label1 label2...>
bigDataUrl <url/relativePath>
barChartColors <color1 color2...>
barChartLabel <label>
barChartMetric <metric>
barChartUnit <unit>
barChartMatrixUrl <url/relativePath>
barChartSampleUrl <url/relativePath>
maxLimit <maximum-bar-value>
Additional settings defined in other sections are also available for displaying bigBarChart tracks. labelFields, defaultLabelFields url urlLabel urls
Example of a bigBarChart track

bigInteract - Pairwise interaction display
type bigInteract
bigDataUrl <url/relativePath>
interactDirectional <true/offsetSource/offsetTarget/clusterSource/clusterTarget>
interactUp <true/false>
Additional settings defined in other sections are also available for displaying bigInteract tracks. maxHeightPixels scoreMin spectrum,
Example of a bigInteract track

pgSnp - Personal Genome SNP track settings
type pgSnp
pgPolyphenPredTab <arg>
pgSiftPredTab <arg>
Example of a Personal Genome SNP track:

vcfTabix - Variant Call Format (indexed by tabix) track settings
type vcfTabix
bigDataUrl <url/relativePath>
bigDataIndex <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:

psl - Sequence alignment tracks settings
type psl <subtype> [otherDb]
blastRef <assembly.table>
colorChromDefault off
pred <assembly.table>
pslSequence <no/all/different>
transMapGene <assembly.table> transMapInfo <table> transMapSrc <assembly.table> transMapTypeDesc <label>
ucscRetroInfo
Additional settings defined elsewhere in this document are also available for displaying psl tracks. baseColorUseSequence, baseColorDefault, chainLinearGap, chainMinScore, indelDoubleInsert, indelQueryInsert, indelPolyA, itemDetailsHtmlTable, matrix, matrixHeader, maxItems, maxWindowToDraw, showCdsAllScales, showCdsMaxZoom, showDiffBasesAllScales, showDiffBasesMaxZoom, spectrum
Examples of psl alignment tracks

chain and netAlign - paired species alignment track settings
type chain <otherDb> otherDb <otherDb>
type netAlign <otherDb> <otherChainTable> otherDb <otherDb>
chainColor <scheme>
chainLinearGap <loose/medium>
chainMinScore <#>
chainNormScoreAvailable <yes/no>
matrix <size> <#,#,#,#,…> matrixHeader <b1,b2,b3,b4> $matrix token in html.
spectrum on
Examples of chain and netAlign tracks

wigMaf - Multiple alignment track settings
type wigMaf <minVal> <maxVal>
frames <table>
irows off
itemFirstCharCase noChange
pairwiseHeight <#>
speciesCodonDefault <species>
speciesDefaultOff <species1> [species2 ...]
Related settings: speciesOrder <species1> [species2 …]
speciesGroups <sgroup1> [sgroup2 …] sGroup_<sgroupN> <species1> [species2 …]
summary <tableName>
treeImage <imageFile>
wiggle <table1> <leftLabel1> <uiLabel1> [table2 leftLabel2 uiLabelN ...]
Examples of wigMaf tracks

expRatio - Microarray expression track settings
type expRatio
expDrawExons on
expScale <#>
expStep <#>
expTable <tableName>
groupings <fileName>
Example of an expRatio track:

snp - Short genetic variants from dbSNP track settings
type bed 6 +
chimpDb <db>
chimpMacaqueOrthoTable <table>
chimpOrangMacOrthoTable <table>
codingAnnoLabel_<table> <text>
codingAnnotations <table>[,table]
defaultGeneTracks <genesTrack>[,genesTrack]
defaultMaxWeight <1|2|3>
hapmapPhase <II|III>
macaqueDb <db>
orangDb <db>
snpExceptions <table>
snpExceptionDesc <table>
snpSeq <table>
snpSeqFile <path>
Additional settings found in the "Item or region tracks" section are also available for displaying snp tracks. maxWindowToDraw
Example of a snp track:

Specialized or rarely used types:

NONE OF THESE ARE FOR HUBS. Nor are any of their settings.

altGraphX - Alternate splicing gene model track settings
type altGraphX
Example of an altGraphX track:

bedDetail - Text extended bed track settings
type bedDetail <#>
Additional settings defined elsewhere in this document are also available for displaying bedDetail tracks. itemRgb, url, urlLabel TODO: Currently almost no settings or configuration options are supported by bedDetail tracks. However, there is very little, in principle, that should prevent adding support for almost all the "Item or region tracks" settings.
Example of a bedDetail track:

clonePos - Genome coverage track settings
type clonePos
Example of a clonePos track:

ctgPos - Physical map contigs track settings
type ctgPos
Example of a ctgPos track:

downloadsOnly - Specialized downloadable file track settings
type downloadsOnly
fileSortOrder ...
Example of a Downloads Only track:

encodeFiveC - Five C Chromatin interaction track settings
type encodeFiveC
interTable <tableName>
interTableKind <label>
Example of an encodeFiveC track:

factorSource - Combined items track settings
type factorSource
sourceTable <table>
inputTrackTable <table>
inputTableFieldDisplay <f1> [f2...]
filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]
motifTable <on>
motifTable <table>
motifPwmTable <table>
motifMapTable <table>
motifMaxWindow <window size>
Example of a factorSource track:

rmsk - Repeat masking track settings
type rmsk
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. maxWindowToDraw, spectrum
Example of a Repeat Masking track:

snake - Self referencing alignment track settings
type snake <db> otherDb <otherDb>
Additional settings found in the "Item or region tracks" section are also available for displaying snake tracks. maxWindowToDraw, spectrum
Example of a snake track:

All tracks have to be assigned to one predefined track group ("Mapping and sequencing", "Genes", etc).
In addition and 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

Predefined major track groupings setting
group <groupId>
Example of a track belonging to a predefined group:

Supertrack (Folders) track 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 …]
controlledVocabulary <pathToFile> <gTag#=mdbVar> [gTag#=mdbVar …]
sortOrder <gTag#=+/-> [gTag#=- …]
fileSortOrder <var=val> [var=val ...]
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: