Track Database Definition

This document summarizes the changes to the UCSC Genome Browser Hub TrackDb specification.

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Date Track Types Link to Doc Change
2026-08-28 bigLolly lollyNoStems Renamed in the documentation, from noStems. The Browser has always + read lollyNoStems, so a track that set noStems drew its + stems as usual. hubCheck takes its list of valid settings from this + page, so it accepted the spelling that did nothing and rejected the one that works. + If your hub sets noStems, change it to lollyNoStems.
2026-08-28 all type The list of valid types on this page now shows only the types a hub can use. + It had been showing the full list, which includes types that only work for tracks + loaded into our own databases. The three hub types missing from the shorter list, + bigGenePred, bigNarrowPeak and vcfPhasedTrio, + have been added.
2026-08-28 all canPack, + configureByPopup, + origAssembly Now listed on this page, and no longer marked as unavailable to hubs. The Browser + reads all three from a hub's trackDb the same way it reads them from ours, so the old + note was wrong. canPack is still marked deprecated: the track type + usually decides whether pack and squish are offered, so you rarely need to set it.
2026-08-28 bigMaf, bigGenePred speciesGroups, + speciesDefaultOff, + speciesCodonDefault, + itemFirstCharCase, + irows, + intronGap Now listed on this page. A bigMaf track is drawn and configured by the same code + as a wigMaf track, so the five multiple-alignment settings have always worked on it, + but only speciesOrder was documented that way. intronGap is + read for every track type that draws linked features, bigGenePred included. Nothing + about their behavior changed.
2026-08-28 bigBed, bigGenePred, bigPsl, bigLolly filterBy Now listed on this page, and no longer marked as unavailable to hubs. The + Browser applies filterBy to bigBed-backed tracks when it loads them, so + it has worked in hubs for some time. If you avoided it because of the old note, you + can use it now.
2026-08-28 bigBed, bigPsl baseColorTickColor Now listed on this page, and no longer marked as unavailable to hubs. It has + always worked in hubs. The entry now also states the requirement that was missing: + the tick color is worked out from each item's own color, so the setting does nothing + unless the track sets colorByStrand. itemRgb does not + satisfy it.
2026-08-28 bigChain, bigMaf, bigBarChart, bigWig chainColor, + chainNormScoreAvailable, + pairwiseHeight, + barChartMatrixUrl, + mouseOverFunction Now listed on this page. All five have worked in hubs for years, but none had an + entry here, so hubCheck reported them as unrecognized settings. + Nothing about their behavior changed.
2026-08-28 bigBed, bigGenePred, bigPsl, bigChain, bigNarrowPeak, bigMaf, vcfTabix spectrum and 25 others Documentation fix: the "For Types" list was wrong for 26 settings, so the docs + named the wrong track types for settings that have always worked. Most named only the + older type and left out its big* counterpart, for example + noScoreFilter said bed while its own example uses + type bigBed 6 +, and the hapCluster* settings said + vcf and not vcfTabix. Six others said "all" for a setting + that only works on item tracks. No browser behavior changed.
2026-08-28 bigPsl pslSequence Removed. This setting has never done anything. The variable it described was + replaced by the baseColorUseSequence + family long before the setting was listed here. Use + baseColorUseSequence and + baseColorDefault instead.

2026-07-31 faceted composite maxCheckboxes Documentation fix: this setting was previously listed here as maxCheckBoxes, with a capital B. Setting names are case sensitive and the browser has always read it as maxCheckboxes, so hubs that used the capitalized spelling fell back to the default of 20 facet values. If your hub sets maxCheckBoxes, change it to maxCheckboxes.

2026-07-08 genomes.txt setting codonTable New codonTable genome-stanza setting (an assembly hub

Date	Track Types	Link to Doc	Change
2026-08-28	bigLolly	lollyNoStems	Renamed in the documentation, from `noStems`. The Browser has always + read `lollyNoStems`, so a track that set `noStems` drew its + stems as usual. `hubCheck` takes its list of valid settings from this + page, so it accepted the spelling that did nothing and rejected the one that works. + If your hub sets `noStems`, change it to `lollyNoStems`.
2026-08-28	all	type	The list of valid types on this page now shows only the types a hub can use. + It had been showing the full list, which includes types that only work for tracks + loaded into our own databases. The three hub types missing from the shorter list, + `bigGenePred`, `bigNarrowPeak` and `vcfPhasedTrio`, + have been added.
2026-08-28	all	canPack, + configureByPopup, + origAssembly	Now listed on this page, and no longer marked as unavailable to hubs. The Browser + reads all three from a hub's trackDb the same way it reads them from ours, so the old + note was wrong. `canPack` is still marked deprecated: the track type + usually decides whether pack and squish are offered, so you rarely need to set it.
2026-08-28	bigMaf, bigGenePred	speciesGroups, + speciesDefaultOff, + speciesCodonDefault, + itemFirstCharCase, + irows, + intronGap	Now listed on this page. A bigMaf track is drawn and configured by the same code + as a wigMaf track, so the five multiple-alignment settings have always worked on it, + but only `speciesOrder` was documented that way. `intronGap` is + read for every track type that draws linked features, bigGenePred included. Nothing + about their behavior changed.
2026-08-28	bigBed, bigGenePred, bigPsl, bigLolly	filterBy	Now listed on this page, and no longer marked as unavailable to hubs. The + Browser applies `filterBy` to bigBed-backed tracks when it loads them, so + it has worked in hubs for some time. If you avoided it because of the old note, you + can use it now.
2026-08-28	bigBed, bigPsl	baseColorTickColor	Now listed on this page, and no longer marked as unavailable to hubs. It has + always worked in hubs. The entry now also states the requirement that was missing: + the tick color is worked out from each item's own color, so the setting does nothing + unless the track sets `colorByStrand`. `itemRgb` does not + satisfy it.
2026-08-28	bigChain, bigMaf, bigBarChart, bigWig	chainColor, + chainNormScoreAvailable, + pairwiseHeight, + barChartMatrixUrl, + mouseOverFunction	Now listed on this page. All five have worked in hubs for years, but none had an + entry here, so `hubCheck` reported them as unrecognized settings. + Nothing about their behavior changed.
2026-08-28	bigBed, bigGenePred, bigPsl, bigChain, bigNarrowPeak, bigMaf, vcfTabix	spectrum and 25 others	Documentation fix: the "For Types" list was wrong for 26 settings, so the docs + named the wrong track types for settings that have always worked. Most named only the + older type and left out its `big` counterpart, for example + `noScoreFilter` said `bed` while its own example uses + `type bigBed 6 +`, and the `hapCluster` settings said + `vcf` and not `vcfTabix`. Six others said "all" for a setting + that only works on item tracks. No browser behavior changed.
2026-08-28	bigPsl	pslSequence	Removed. This setting has never done anything. The variable it described was + replaced by the baseColorUseSequence + family long before the setting was listed here. Use + `baseColorUseSequence` and + baseColorDefault instead.
2026-07-31	faceted composite	maxCheckboxes	Documentation fix: this setting was previously listed here as `maxCheckBoxes`, with a capital B. Setting names are case sensitive and the browser has always read it as `maxCheckboxes`, so hubs that used the capitalized spelling fell back to the default of 20 facet values. If your hub sets `maxCheckBoxes`, change it to `maxCheckboxes`.
2026-07-08	genomes.txt setting	codonTable	New `codonTable` genome-stanza setting (an assembly hub