Track Database Definition

Track Database Definition

How to declare Dataset Display Settings in the Genome Browser

Hub contributors should use the Hub Track specific version of this document.

This document describes how to declare dataset display characteristics in the Genome Browser through trackDb settings. Introducing new 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 stored in a database called the "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 bed 6
        shortLabel Example Data
        longLabel The data in this track is format "bed 6".    

Every track should have these four settings. The key of this track (myFirstTrack) is the name of the dataset. If the data is loaded into a MySQL table then the track name is almost always the table name. If the data is in one of the remote indexed file types (e.g. bigWig, bam, etc.) then the name is typically the root file name. However, this is a key to the track so it must be unique within the Genome Browser. (Data hubs need only declare track names unique to their 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.

  1. Common trackDb settings
  2. Settings by track type – with examples
  3. Grouping tracks into sets and hierarchies – with examples
  4. Special settings for custom tracks
  5. Obscure or special cases – (aka Rejections)
  6. Table of Contents
 Open/close all details.
  Common trackDb settings
 Common Settings
track
type
shortLabel
longLabel
visibility
html

 Common Optional Settings
bigDataUrl <url/relativePath>
boxedCfg <on/off>
color <red,green,blue>
altColor <red,green,blue>
chromosomes <chr1,chr2,...>
configureByPopup <on/off>
dataVersion <str>
Related settings:
directUrl <url>
iframeUrl <url>
iframeOptions <string>
otherDb <otherDb>
origAssembly <db>
pennantIcon <icon> [html [tip]]
priority <float>
release <alpha/beta/public>[,beta/public]
table <tableName>
tableBrowser <off/on> [table1 ...]
url <url>
urlLabel <label>
idInUrlSql <sql for id>
urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...
wgEncode on
  Settings by track type

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>
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 >
exonArrowsDense <off/on>
itemDetailsHtmlTable <table>
itemImagePath <path> <suffix>
itemBigImagePath <path> <suffix>
linkIdInName on
mafTrack <trackName>
nextExonText <str>
prevExonText <str>
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...>
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 - Compressed Sequence Alignment track settings
type bam
bigDataUrl <url/relativePath>
Related settings:
bamColorMode <strand/gray/tag/off>
bamSkipPrintQualScore .
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.

baseColorUseSequence, baseColorDefault, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Example for bam 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>
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:


 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 …]
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:
  Grouping tracks into sets and hierarchies

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:
  Special settings for custom tracks
 Custom track specific settings
genome
offset

The following trackDb style settings are only set internally by the hgCustom CGI code.

browserLines
dataUrl
dbTrackType
fieldCount
firstItemPos
htmlFile
htmlUrl
initialPos
inputType
itemCount
mafFile
maxChromName
origTrackLine
tdbType
wibFile
wigFile
   Obscure or special case settings. (aka Rejections)

Rejected "types":

axt – rare bed 3 variant (replaced with netAlign?), panTro1.axtNetHg16

drosophila/dp1/trackDb.ra:type axt dm1

human/hg13/trackDb.ra:type axt mm3

human/hg15/trackDb.ra:type axt mm3

worm/ce1/trackDb.ra:type axt cb1

worm/ce2/trackDb.ra:type axt cb1

bedLogR – encode 1% test only??? Not found with tdbQuery from *

human/encodeTest/wgEncodeMetaCheckTest.ra

chromGraph - ??? Not found in tdbQuery -strict from *

gff http://genome.ucsc.edu/FAQ/FAQformat.html#format3

Not found in tdbQuery -strict from *

gtf http://genome.ucsc.edu/FAQ/FAQformat.html#format4

Not found in tdbQuery -strict from *

maf – replaced by wigMaf hg17, tdbQuery -strict: 1 track: fr1.tbaFishBirdCFTR

http://genome.ucsc.edu/FAQ/FAQformat.html#format5

net but not netAlign - custom only??? Not found with tdbQuery non strict

sample – RARE bed variant, hg15.affyTranscriptome, Affymetrix Transcriptome

hg15.hg15Mm3L

Completely replaced by type wig and more recently bigWig

List of Miscellaneous Specal Case, Deprecated, Rejected or Rarely Used Settings

Rejected settingsFor TypesReason
accession all ENCODE only ENCODE only; DEPRCATED (replaced with mdb )
canPack <off/on> all NOT FOR HUBS. Deprecated.

Almost tracks can be displayed in the five standard visibilities. However on some track types such as wiggles, squish and pack offer no real advantage over dense and full. By default, these tracks will not offer the less valuable visibilities. Nevertheless, you can make your track offer these visibilility choices by turning canPack on. Note: subtracks of composites will always offer all five choices.

Example:

   canPack on
cdsDrawDefaultgenePred There are a number of occurrences of cdsDrawDefault in our trackDbs, always set to ‘genomic\ codons ‘. However, I have found no documentation and no code that references this setting.
cdsDrawOptionspsl I have found no documentation and no code that references this setting. Also, I do not see it in our trackDbs.
cdsEvidence genePred Used by JK experimental tracks only as either jkgTxCdsEvidence or jkgTxCdsEvidence2. This will show an evidence table named in the setting.
cell bed, bedGraph ENCODE only Obsolete: replaced with metaDb.
chip expRatio, bed ENCODE only DROP (no takers in any of our trackDb.ra files)
dateSubmitted bedGraph, bed ENCODE only Obsolete: replaced with metaDb.
dateUnrestricted bed ENCODE only Obsolete: replaced with metaDb.
db chain, netAlign, genePred, bed 3 Not found in any of our trackDb.ras. Further, this is the same as assembly so implicit.
dbProfileall In hg18 experimental and cancerGenomics only.
dividers all OBSOLETE: use sortOrder instead.
endFudgebed Special case for hg17 HGSV Discordant (variation) tracks. Used in hgc to fudge chromEnd, I think.
ensArchivegenePred Only in danRer4 Ensembl NonCoding to generate an Ensembl URL.
ensemblTranscriptIdUrl genePred ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
ensemblGeneIdUrl genePred ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
ensemblIdUrl genePred ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
expProbeTable expRatio Can't find code that supports this.Rare: only in human. affyHumanExon "Affy All Exon"
extTableall This setting points to a one record table that holds the external filename. This should be replaced by: track, table or bigDataUrl.

(rare bigWig hg18.brTestPlus experimental track)

extraFieldsbed OBSOLETE: replaced by looking up "as" table description. However, that method does not allow for:
  • selective inclusion/exclusion of fields
  • reordering fields
  • formatting titles
filePosall Can't find this in any of our trackDb.ra files.
filterTopScorers bed5FloatScoreWithFdr, bed5FloatScore ENCODE only Currently only used by pilot encode 1%.

Presents user option to limit to the top scoring N items. Might be useful in other MySQL table based tracks but how valuable is it?

gainColor
lossColor
bed ENCODE only Currently only used by pilot encode 1% in hg17.encodeDless.

Provides special color for "gain" and "loss" items.

graphType bedGraph Not found in code. Probably typo of graphTypeDefault. (rare hg18.encodeRegulomeDnaseArray)
hgGenegenePred Cannot find code for this. No effect. ???
informantgenePred Special setting for N-SCAN genes. Swapped into html description page.
inputTracksSubgroupDisplay bed, factorSource ENCODE only Only in hg18/hg19 wgEncodeReg*Clustered tracks. In code #ifdef TO_BE_REMOVED.
itemAttrTblgenePred Only used in borEut13. transMapRefGene.
linesAtchromGraph Unused track type (tdbQuery -strict).
longlabelgenePred Typo, should be longLabel.
longLabelClip all Only used in sacCer3 (tdbQuery -strict).
mafDotwigMaf Can't find this in any of our trackDb.ra files and only supported as cart var.
mafDotDefault wigMaf Can't find this in any of our trackDb.ra files.
mapDispatcher expRatio Only hg17 group "x" [tingwang 2007] and not in C.
maxScorebroadPeak Obsolete, replaced with scoreFilterLimits.
all ENCODE only OBSOLETE: replaced by metaDb. Currently only way for datHubs to have metadata dropdowns. Used by WashU hubs.
mgiUrlbed Special case variant of url used by no current tracks (tdbQuery -strict).
mgiUrlLabelbed Special case variant of url used by no current tracks (tdbQuery -strict).
minMaxchromGraph Unused track type (tdbQuery -strict).
minScore bed, narrowPeak, broadPeak Obsolete, replaced with scoreFilterLimits.
msaTable wig, wigMafProt, wigMaf Only hiv tracks use this. Code in wigMaf display and is used to look up species order.
ncbiAccXrefbed Special case used by hg17/hg18 kiddEichler tracks. Names a table to convert kiddEichler IDs to NCBI IDs and print links.
nextItemButton all This setting lets you override the Browser wide setting to disable nextItem arrows (which is off by default). When this is on, the nextItem arrows will show up for your track. The opposite does not seem to be the case, where nextItems are enabled, but you want to exclude them from your track.
noInheritall This one should be OBSOLETE but there continue to be edge cases where this setting has some affect. Currently only 2 places this is read this:

  1. in hdb to makesuperChildren inherit settings from their supertrack. This is done by putting the super settings into the child's settings hash.
  2. tdbQuery where it appears to have no affect.
nonBedFieldsLabel bigBed OBSOLETE when bigBed has "as" definitions. Instead, the extraFieldsPrint should pick up the non-standard bed fields straight from the as definition.
notNCBIbed Only used in drosophila dm2/dm3. Referenced in hgc.c code.
ococcibed Not referenced in any of our trackDb.ra files or in code.
otherOrgchain, netAlign Typo: should be otherDb.
onlyVisibility all Not universally supported (rightClick/subtrack cfg, etc.) so deprecate or else expand. This setting restricts the visibility options of a track to only one setting such as "full". (rare hg19.lincRNAsAllCellTypeTopView)
otherDbTablebed Special case for Jackson lab's QTL (Quantitative Trait Locus) tracks.
pairedEndUrlFormatbed Special case only used on kiddEichler track. This is another external URL variant.
pairwisewigMaf Deprecate, replaced by summary.
patDbexpRatio Only hg17 group "x" [jzhu 2007] and not referenced in C.
patKeyexpRatio Only hg17 group "x" [jzhu 2007] and not referenced in C.
patTableexpRatio Only hg17 group "x" [jzhu 2007] and not referenced in C.
bed Special only used in hg18/hg19 Genome Variants so far.

This setting is used to name one or more tables that hold links to phenotype and other databases for pgSnps. Each table must have chrom, chromStart, chromStop, name and srcUrl as fields. The links will be seen in the bed item details page and will be looked up in each listed table by item location.

Example:

   pgDbLink pgKb1PhenCode pgKb1Snpedia pgKb1Hgmd
privatebed Only used in human/hg7/trackDb.ra, and not even there using tdbQuery -strict. Prevents access to data by removing from trackList when doing "pruneEmpties". Gotta wonder when the track is ever seen in the browser or why it is a track at all.
pslTablebed Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same illuminaProbesAlign when track is "illuminaProbesAlign".) Used for making an hgcAnchor htcIlluminaProbesAlign.
pubsArticleTable bed, psl Special for publications track.
pubsMarkerTablebed, psl Special for publications track.
pubsPslTrack bed, psl Special for publications track.
pubsSequenceTablebed, psl Special for publications track.
refSeqAnnoVersiongenePred Special for rheMac2.refSeqAnno track. Not found in code.
scoreFilterMax bed, bedLogR, peptideMapping, bigBed OBSOLETE: replaced by scoreFilterLimits
searchMethod bed Error. Should be part of searchTable stanza, not track stanza.

TODO: Document searchTable stanza.

searchTypebed Error. Should be part of searchTable stanza, not track stanza.

TODO: Document searchTable stanza.

selectSubject psl Special only used in hiv(only used by hiv and h1n1. (Just h1n1 according to tdbQuery -strict).
seqTablebed Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same illuminaProbesSeq when track is "illuminaProbesAlign".) Used for making an hgcAnchor htcIlluminaProbesAlign.
settingsByView all OBSOLETE: replaced with "view in the middle" view as separate track.
snpTable <table> bed gwasCatalog only Special for gwasCatalog: table used to map dbSNP IDs to genomic coords
snpVersion bed gwasCatalog only Special for gwasCatalog: dbSNP build number of table used to map dbSNP IDs to genomic coords
speciesTarget wigMaf OBSOLETE. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with
#define BRANEY_SAYS_USETARG_IS_OBSOLETE.
speciesTreewigMaf OBSOLETE. Replaced by treeImage. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with
#define BRANEY_SAYS_USETARG_IS_OBSOLETE.
speciesUseFile <fileName> wigMaf

Deprecated

Much more rarely used, this setting can replace speciesOrder and speciesGroups. Set the speciesUseFile to a path relative to the apache cgi-bin. The file should contain a single species name as the first word of each line.

Example:

    speciesUseFile speciesLists/conserved8Way.txt
stripPrefixbam Not yet implemented? Only on hg18.oneKGHighCovSeq experimental track.
subgroupsbed Typo: should be subGroups.
subTrackall OBSOLETE: replaced with parent.
symbolTable bed, genePred In hgTracks, flyBaseGeneName() methods, if an item name is found in this symbol table, the symbol name will be shown instead. Found in drosophila and strangely rn4 RGD Genes (but table named in rn4 does not have a symbol column. Instead, symbol lookup is hard-coded to rgdGene2ToSymbol).
txInfogenePred Only seems to be used in experimental tracks in hg18 and mm8.
urlNamegenePred Not referenced in code and rarely used. (e.g. hg18: encodePseudogeneConsensus, encodePseudogeneYale).
url2bed Special cased second URL used much like url.
url2Labelbed Special cased second URL label used much like urlLabel.
useScorebed, factorSource, bed5FloatScore, broadPeak Deprecate: replaced with spectrum as a slighly less obscurely named setting.
vegaGeneIdUrl genePred ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
vegaTranscriptIdUrl genePred ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
visibilityViewDefaultsall OBSOLETE since view in the middle change. LOSE
wgEncodeGencodeVersion genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeAttrs genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeExonSupport genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeGeneSource genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeTranscriptSource genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodePdb genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodePubMed genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeRefSeq genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeTag genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeTranscriptSupport genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeUniProt genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodePolyAFeature genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeAnnotationRemark genePred ENCODE Gencode Only Special for ENCODE Gencode.
wgEncodeGencodeTranscriptionSupportLevel genePred ENCODE Gencode Only Special for ENCODE Gencode.
yLinOnOffwigMaf

Typo: should be yLineOnOff.

yalePseudoAssoc all ENCODE Gencode Only Special for ENCODE Gencode.
yalePseudoUrl all ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.
yaleUrl all ENCODE Gencode Only Special for ENCODE Gencode to generate external URL.