1c07e6e9103123809e420560f2ebf370dde996ea jcasper Sun Jan 11 21:24:24 2026 -0800 Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs are actually drawn in arc mode, refs #36774 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html index 3ff4a42da42..359965d1fd1 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html @@ -1,2763 +1,2771 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <META name="description" content="UCSC Track Database Definition"> <META name="keywords" content="tracDb, tracks, UCSC, bioinformatics"> <TITLE>UCSC Track Database Definition</TITLE> <LINK REL="STYLESHEET" HREF="/style/HGStyle.css"> <LINK REL="STYLESHEET" HREF="trackDbDoc.css"> <script type="text/javascript" src="/js/jquery.js"></script> <script type="text/javascript" src="/js/staticDoc.js"></script> <script type="text/javascript" src="/js/utils.js"></script> <script type="text/javascript" src="trackDbDoc.js"></script> <script type="text/javascript"> $(document).ready(function() { //tdbDoc.library.checkup(); // Run this test during development only // TOC Self assembly EXPERIMENTAL tdbDoc.tocAssemble( 0, ["bed_flavors","parent_supertrack", "parent_view","parent_container"] ); tdbDoc.documentLoad(); }); </script> </HEAD> <BODY> <A NAME="TOP"></A> <!-- Format everthing inside this narrower "pageWidth" window --> <div class="pageWidth"> <!--#include virtual="../../../cgi-bin/hgMenubar"--> <!--Content Tables--> <!--outer table is for border purposes--> <div class="contentBorder"> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Track Database Definition</div> </div> <div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span> This document has been deprecated. For the latest TrackDb settings see the <a href="trackDbHub.html">Track Hub definition doc</a>.<br><br> This change was done to remove redundancy. This page existed to document all trackDb settings including internal ones whereas the Track Hub document covered only settings compatible with hubs. However, all new settings developed are now hub-compatible.</p> </div> <!-- Finally to the content --> <div class="borderGuard"> <DIV class="trackDbDoc_intro"> <H1>Track Database Definition</H1> <H2>How to declare Dataset Display Settings in the Genome Browser</H2> <P><I>Hub contributors should use the <A HREF="trackDbHub.html">Hub Track</A> specific version of this document.</I></P> <P>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.</P> <P>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:</P> <pre> track myFirstTrack type bed 6 shortLabel Example Data longLabel The data in this track is format "bed 6". </pre> <P>Every track should have these four settings. The key of this track (<code>myFirstTrack</code>) is the name of the dataset. If the data is loaded into a MariaDB 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. </P> </DIV> <P>The remainder of this document is divided into the following sections and should be used as a ready reference.</P> <OL> <LI><A HREF="#commonSettings">Common trackDb settings</A></LI> <LI><A HREF="#settingsByType">Settings by track type</A> – with examples <UL> <LI><A HREF="#bed_-_Item_or_Region_Track_Settings">bed/bigBed</A>: Item or region tracks</LI> <LI><A HREF="#wig_-_Signal_Graphing_Track_Settings">wig/bigWig/bedGraph</A>: Signal graphing tracks</LI> <LI><A HREF="#genePred">genePred/bigGenePred</A>: Gene models and predictions</LI> <LI><A HREF="#bam">bam/cram</A>: Compressed Sequence Alignment/Map tracks</LI> <LI><A HREF="#pgSnp">pgSnp</A>: Personal Genome SNP tracks</LI> <LI><A HREF="#vcfTabix">vcfTabix</A>: Variant Call Format</LI> <LI><A HREF="#vcfPhasedTrio">vcfPhasedTrio</A>: Variant Call Format Trios</LI> <LI><A HREF="#psl">psl/bigPsl</A>: Sequence alignments</LI> <LI><A HREF="#chain">chain/bigChain and netAlign</A>: Paired sequence alignments</LI> <LI><A HREF="#wigMaf">wigMaf/bigMaf</A>: Multiple alignments</LI> <LI><A HREF="#expRatio">expRatio</A>: Microarray expression data</LI> <LI><A HREF="#snp">snp</A>: Short genetic variants from dbSNP</LI> <LI><A HREF="#bigBarChart">barChart/bigBarChart</A>: Categorical values over a region</LI> <LI><A HREF="#bigInteract">interact/bigInteract</A>: Pairwise interactions</LI> <LI><A HREF="#bigLolly">bigLolly</A>: Lollipop charts</LI> <LI><A HREF="#hic">hic</A>: Hi-C contact matrices</LI> <LI><A HREF="#rareTypes">Specialize or rarely used</A>:<BR> <A HREF="#altGraphX">altGraphX</A>, <A HREF="#bedDetail">bedDetail</A>, <A HREF="#clonePos">clonePos</A>, <A HREF="#ctgPos">ctgPos</A>, <A HREF="#downloadsOnly">downloadsOnly</A>, <A HREF="#encodeFiveC">encodeFiveC</A>, <A HREF="#factorSource">factorSource</A>, <A HREF="#rmsk">rmsk</A> and <A HREF="#snake">snake</A>.</LI> </UL></LI> <LI><A HREF="#groupingTracks">Grouping tracks into sets and hierarchies</A> – with examples <UL> <LI><A HREF="#group">Predefined major track groupings</A></LI> <LI><A HREF="#superTrack">Supertracks (Folders)</A></LI> <LI><A HREF="#compositeTrack">Composite Tracks</A> <UL> <LI><A HREF="#subGroups">Subgroups</A></LI> <LI><A HREF="#view">Views</A></LI> </UL></LI> <LI><A HREF="#aggregate">Aggregate or Overlay Tracks: multiWig</A></LI> </UL></LI> <LI><A HREF="#customTracks">Special settings for custom tracks</A></LI> <LI><A HREF="#loosers">Obscure or special cases</A> – (aka Rejections)</LI> <LI><A HREF="#toc">Table of Contents</A></LI> </OL> <IMG class='toggle all' /> <I>Open/close all details.</I> </div></div> <!-- Next section --> <div class="contentBorder"> <A name="commonSettings"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Common trackDb settings</div> </div> <div class="borderGuard"> <TABLE class="settingsTable" id="Common_Settings"> <THEAD><TR><TD><DIV ID="commonSettings_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection' /> Common Settings</TH></TR> <TR VALIGN=TOP><TD class="track"><A name="track"></A><IMG class='toggle detail'> <div class="format"><code>track</code></div> </TD></TR> <TR VALIGN=TOP><TD class="type"><A name="type"></A><IMG class='toggle detail'> <div class="format"><code>type</code></div> </TD></TR> <TR VALIGN=TOP><TD class="shortLabel"><A name="shortLabel"></A><IMG class='toggle detail'> <div class="format"><code>shortLabel</code></div> </TD></TR> <TR VALIGN=TOP><TD class="longLabel"><A name="longLabel"></A><IMG class='toggle detail'> <div class="format"><code>longLabel</code></div> </TD></TR> <TR VALIGN=TOP><TD class="visibility"><A name="visibility"></A><IMG class='toggle detail'> <div class="format"><code>visibility</code></div> </TD></TR> <TR VALIGN=TOP><TD class="html"><A name="html"></A><IMG class='toggle detail'> <div class="format"><code>html</code></div> </TD></TR> </TABLE> <BR> <A name="commonLessFrequent"></A> <TABLE class="settingsTable" id="Common_Settings_-_less_frequent"> <THEAD><TR><TD><DIV ID="lessCommon_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH> <IMG class='toggle oneSection' /> Common Optional Settings </TH> </TR> <TR VALIGN=TOP><TD class="bigDataUrl"><A name="bigDataUrl"></A><IMG class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="boxedCfg"><A name="boxedCfg"></A><IMG class='toggle detail'> <div class="format"><code>boxedCfg <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="color"><A name="color"></A><IMG class='toggle detail'> <div class="format"><code>color <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="altColor"><A name="altColor"></A><IMG class='toggle detail'> <div class="format"><code>altColor <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromosomes"><A name="chromosomes"></A><IMG class='toggle detail'> <div class="format"><code>chromosomes <chr1,chr2,...></code></div> </TD></TR> <TR VALIGN=TOP><TD class="configureByPopup"><A name="configureByPopup"></A> <IMG class='toggle detail'> <div class="format"><code>configureByPopup <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="darkerLabels"><A name="darkerLabels"></A><IMG class='toggle detail'> <div class="format"> <code>darkerLabels on</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="dataVersion"><A name="dataVersion"></A><IMG class='toggle detail'> <div class="format"><code>dataVersion <str></code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="directUrl"> <A name="directUrl"></A> <A name="hgsid"></A><IMG class='toggle detail setA'> <div class="format"><I>Related settings:</I><BR> <code>directUrl <url></code><div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="hgsid"> <IMG class='toggle detail setA'> <div class="format"><code>hgsid on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="iframeUrl"><A name="iframeUrl"></A><IMG class='toggle detail'> <div class="format"><code>iframeUrl <url></code></div> </TD></TR> <TR VALIGN=TOP><TD class="iframeOptions"><A name="iframeOptions"></A><IMG class='toggle detail'> <div class="format"><code>iframeOptions <string></code></div> </TD></TR> <TR VALIGN=TOP><TD class="mouseOver"><A name="mouseOver"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">mouseOver <pattern></code></div> </TD></TR> <TR VALIGN=TOP><TD class="mouseOverField"><A name="mouseOverField"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">mouseOverField <fieldName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="multiRegionsBedUrl"><A name="multiRegionsBedUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">multiRegionsBedUrl</code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherDb"><A name="otherDb"></A><IMG class='toggle detail'> <div class="format"><code>otherDb <otherDb></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"></A><IMG class='toggle detail'> <div class="format"><code>otherTwoBitUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="origAssembly"><A name="origAssembly"></A><IMG class='toggle detail'> <div class="format"><code>origAssembly <db></code></div> </TD></TR> <TR VALIGN=TOP><TD class="pennantIcon"><A name="pennantIcon"></A><IMG class='toggle detail'> <div class="format"><code>pennantIcon <iconFile>/<text color> [html [tip]]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="priority"><A name="priority"></A><IMG class='toggle detail'> <div class="format"><code>priority <float></code></div> </TD></TR> <TR VALIGN=TOP><TD class="release"><A name="release"></A><IMG class='toggle detail'> <div class="format"><code>release <alpha/beta/public>[,beta/public]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="table"><A name="table"></A><IMG class='toggle detail'> <div class="format"><code>table <tableName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="tableBrowser"><A name="tableBrowser"></A><IMG class='toggle detail'> <div class="format"><code>tableBrowser <off/on/noGenome/tbNoGenome> [table1 ...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="url"> <A name="url"></A> <A name="urlLabel"></A> <A name="idInUrlSql"></A><IMG class='toggle detail'> <div class="format"> <code>url <url></code><BR> <code>urlLabel <label></code><BR> <code>idInUrlSql <sql for id></code></div> </TD></TR> <TR VALIGN=TOP><TD class="urls"><A name="urls"></A><IMG class='toggle detail'> <div class="format"> <code>urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="skipEmptyFields"><A name="skipEmptyFields"></A><IMG class='toggle detail'> <div class="format"> <code>skipEmptyFields on</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="skipFields"><A name="skipFields"></A><IMG class='toggle detail'> <div class="format"> <code>skipFields <fieldName1>,<fieldName2> ...</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="sepFields"><A name="sepFields"></A><IMG class='toggle detail'> <div class="format"> <code>sepFields <fieldName1>,<fieldName2> ...</code><BR> </div> </TD></TR> <TR VALIGN=TOP> <TD class="wgEncode"><A name="wgEncode"></A><IMG class='toggle detail'> <div class="format"><code>wgEncode on</code></div> </TD></TR> </TABLE> </div></div> <!-- Next section --> <div class="contentBorder"> <A name="settingsByType"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Settings by track type</div> </div> <div class="borderGuard"> <P>Many settings are valid only for certain types of tracks. These track types are described below along with the settings specific to their types.</P> <A name="bed"><A name="bigBed"></A> <TABLE class="settingsTable" id="bed_-_Item_or_Region_Track_Settings"> <THEAD><TR><TD><DIV ID="bed_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bed/bigBed - Item or region track settings </TH></TR> <TR VALIGN=TOP><TD class="bed"><IMG class='toggle detail'> <div class="format"> <code>type bed <3-12> [+/.]</code><BR> <code>type bigBed <3-12> [+/.]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bed_flavors"> <A name="bed5FloatScore"></A> <A name="bedRnaElements"></A> <A name="broadPeak"></A> <A name="coloredExon"></A> <A name="gvf"></A> <A name="ld2"></A> <A name="narrowPeak"></A> <A name="peptideMapping"></A><IMG class='toggle detail'> <div class="format"> <code>type bed5FloatScore</code><BR> <code>type bedRnaElements</code><BR> <code>type broadPeak</code><BR> <code>type coloredExon</code><BR> <code>type gvf</code><BR> <code>type ld2</code><BR> <code>type narrowPeak</code><BR> <code>type peptideMapping</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="colorByStrand"><A name="colorByStrand"></A><IMG class='toggle detail'> <div class="format"><code>colorByStrand <red,green,blue> <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="compareGenomeLinks"><A name="compareGenomeLinks"></A> <IMG class='toggle detail'> <div class="format"><code>compareGenomeLinks <db[.table[.column]]=label> [db[.table[.column] =label …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="denseCoverage"><A name="denseCoverage"></A><IMG class='toggle detail'> <div class="format"><code>denseCoverage <maxVal></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelOnFeature"><A name="labelOnFeature"></A><IMG class='toggle detail'> <div class="format"><code>labelOnFeature <on/off></code></div> </TD></TR> <tr valign=top><td class="extraDetailsTable"><a name="extraDetailsTable"></a><img class='toggle detail'> <div class="format"><code class="level-deprecated">extraDetailsTable <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="extraTableFields"><a name="extraTableFields"></a><img class='toggle detail'> <div class="format"><code class="level-deprecated">extraTableFields <fieldName1|table title,fieldName2|table title,...></code> </div> </td></tr> <tr valign=top><td class="detailsStaticTable"><a name="detailsStaticTable"></a><img class='toggle detail'> <div class="format"><code class="level-new">detailsStaticTable <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="detailsDynamicTable"><a name="detailsDynamicTable"></a><img class='toggle detail'> <div class="format"><code class="level-new">detailsDynamicTable <fieldName1|table title,fieldName2|table title,...></code> </div> </td></tr> <TR VALIGN=TOP><TD class="exonArrows"><A name="exonArrows"></A><IMG class='toggle detail'> <div class="format"><code>exonArrows <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="exonNumbers"><A name="exonNumbers"></A><IMG class='toggle detail'> <div class="format"><code>exonNumbers <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="Filter"> <A name="Filter"></A> <A name="scoreFilter"></A> <A name="pValueFilter"></A> <A name="qValueFilter"></A> <A name="signalFilter"></A> <A name="FilterLimits"></A> <A name="FilterByRange"></A><IMG class='toggle detail'> <div class="format"> <code><column>Filter <low>[:<high>]</code><BR> <code>scoreFilter <low>[:<high>]</code><BR> <code>pValueFilter</code><BR> <code>qValueFilter</code><BR> <code>signalFilter</code><BR> <code><column>FilterLimits <low>[:<high>]</code><BR> <code><column>FilterByRange <off/on></code> </div> </TD></TR> <TR VALIGN=TOP><TD class="filter"><A name="filter"> <A name="filter.fieldName"></A> <A name="filterLimits.fieldName"></A> <A name="filterByRange.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>filter.<fieldName> <default integer></code><BR> <code>filterByRange.<fieldName> <off/on></code><BR> <code>filterLimits.<fieldName> <low>[:<high>]</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="filterText"><A name="filterText"> <A name="FilterText.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>filterText.<fieldName> <default search string></code><BR> <code>filterType.<fieldName> <wildcard/regexp></code><BR> </div> <TR VALIGN=TOP><TD class="filterValues"><A name="filterValues"> <A name="filterValues.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>filterValues.<fieldName> <value1,value2,value3...></code><BR> <code>filterValuesDefault.<fieldName> <value1,value2,value3...></code><BR> <code>filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd></code><BR> </div> <TR VALIGN=TOP><TD class="filterLabel"><A name="filterLabel"> <A name="filterLabel.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>filterLabel.<fieldName> <label></code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="highlight"><A name="highlight"> <A name="highlight.fieldName"></A> <A name="highlightLimits.fieldName"></A> <A name="highlightByRange.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>highlight.<fieldName> <default integer></code><BR> <code>highlightByRange.<fieldName> <off/on></code><BR> <code>highlightLimits.<fieldName> <low>[:<high>]</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="highlightText"><A name="highlightText"> <A name="FilterText.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>highlightText.<fieldName> <default search string></code><BR> <code>highlightType.<fieldName> <wildcard/regexp></code><BR> </div> <TR VALIGN=TOP><TD class="highlightValues"><A name="highlightValues"> <A name="highlightValues.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code>highlightValues.<fieldName> <value1,value2,value3...></code><BR> <code>highlightValuesDefault.<fieldName> <value1,value2,value3...></code><BR> <code>highlightType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd></code><BR> </div> <TR VALIGN=TOP><TD class="highlightColor"><A name="highlightColor"></A> <A name="highlightColor"</A><IMG class='toggle detail'> <div class="format"> <code class="level-full">highlightColor <#hexcolor></code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="filterBy"><A name="filterBy"></A><IMG class='toggle detail'> <div class="format"><code>filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="itemRgb"><A name="itemRgb"></A><IMG class='toggle detail'> <div class="format"><code>itemRgb on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxItems"><A name="maxItems"></A><IMG class='toggle detail'> <div class="format"><code>maxItems <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowCoverage"> <A name="maxWindowCoverage"></A><IMG class='toggle detail'> <div class="format"><code>maxWindowCoverage <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowToDraw"> <A name="maxWindowToDraw"></A><IMG class='toggle detail'> <div class="format"><code>maxWindowToDraw <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="minGrayLevel"><A name="minGrayLevel"></A><IMG class='toggle detail'> <div class="format"><code>minGrayLevel <1-9></code></div> </TD></TR> <TR VALIGN=TOP><TD class="noScoreFilter"><A name="noScoreFilter"></A><IMG class='toggle detail'> <div class="format"><code>noScoreFilter on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="spectrum"> <A name="spectrum"></A> <A name="scoreMax"></A> <A name="scoreMin"></A><IMG class='toggle detail'> <div class="format"> <code>spectrum on</code><BR> <code>scoreMax <integer></code><BR> <code>scoreMin <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="thickDrawItem"><A name="thickDrawItem"></A><IMG class='toggle detail'> <div class="format"><code>thickDrawItem <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="decorator"><A name="decorator"></A><IMG class='toggle detail'> <div class="format"><code>decorator.*</code></div> </TD></TR> </TABLE> <TABLE class="settingsTable" id="Item_or_Region_Track_Settings_-_less_frequent"> <TR VALIGN=TOP><TH><A name="item_lessFrequent"></A> <IMG class='toggle oneSection' /> Less frequently used item track settings </TH></TR> <TR VALIGN=TOP><TD class="bedFilter"><A name="bedFilter"></A><IMG class='toggle detail'> <div class="format"><code>bedFilter on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bedNameLabel"><A name="bedNameLabel"></A><IMG class='toggle detail'> <div class="format"><code>bedNameLabel <label></code></div> </TD></TR> <TR> <TR class="related1st" VALIGN=TOP><TD class="baseColorUseSequence"> <A name="baseColorUseSequence"></A><IMG class='toggle detail setB'> <div class="format"><I>Related settings:</I><BR> <code>baseColorUseSequence <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="baseColorUseCds"> <A name="baseColorUseCds"></A><IMG class='toggle detail setB'> <div class="format"><code>baseColorUseCds <given></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="baseColorDefault"> <A name="baseColorDefault"></A><IMG class='toggle detail setB'> <div class="format"><code>baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="baseColorTickColor"> <A name="baseColorTickColor"></A><IMG class='toggle detail setB'> <div class="format"><code>baseColorTickColor <lighterShade/contrastingColor></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="showDiffBasesAllScales"> <A name="showDiffBasesAllScales"></A><IMG class='toggle detail setB'> <div class="format"><code>showDiffBasesAllScales on</code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="showDiffBasesMaxZoom"> <A name="showDiffBasesMaxZoom"></A><IMG class='toggle detail setB'> <div class="format"><code>showDiffBasesMaxZoom <basesPerPixel></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="showCdsAllScales"> <A name="showCdsAllScales"></A><IMG class='toggle detail setB'> <div class="format"><code>showCdsAllScales</code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="showCdsMaxZoom"> <A name="showCdsMaxZoom"></A><IMG class='toggle detail setB'> <div class="format"><code>showCdsMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="exonArrowsDense"> <A name="exonArrowsDense"></A><IMG class='toggle detail'> <div class="format"><code>exonArrowsDense <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="itemDetailsHtmlTable"> <A name="itemDetailsHtmlTable"></A><IMG class='toggle detail'> <div class="format"><code>itemDetailsHtmlTable <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="itemImagePath"> <A name="itemImagePath"></A> <A name="itemBigImagePath"></A><IMG class='toggle detail'> <div class="format"><code>itemImagePath <path> <suffix></code><BR> <code>itemBigImagePath <path> <suffix></code></div> </TD></TR> <TR VALIGN=TOP><TD class="linkIdInName"><A name="linkIdInName"></A><IMG class='toggle detail'> <div class="format"><code>linkIdInName on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="mergeSpannedItems"><A name="mergeSpannedItems"></A><IMG class='toggle detail'> <div class="format"><code>mergeSpannedItems <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="mafTrack"><A name="mafTrack"></A><IMG class='toggle detail'> <div class="format"><code>mafTrack <trackName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="nextExonText"> <A name="nextExonText"></A> <A name="prevExonText"></A><IMG class='toggle detail'> <div class="format"> <code>nextExonText <str></code><BR> <code>prevExonText <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="scoreLabel"><A name="scoreLabel"></A><IMG class='toggle detail'> <div class="format"><code>scoreLabel <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showTopScorers"> <A name="showTopScorers"></A><IMG class='toggle detail'> <div class="format"><code>showTopScorers #</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bed_example"> <A name="bed_Examples"></A><IMG class='toggle detail'> <div class="format"><B>Examples of item base types</B></div> </TD></TR> </TABLE> <BR><BR> <A name="wig"><A name="bigWig"><A name="bedGraph"> <TABLE class="settingsTable" id="wig_-_Signal_Graphing_Track_Settings"> <THEAD><TR><TD><DIV ID="wig_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> wig,bigWig - Signal graphing track settings </TH></TR> <TR VALIGN=TOP><TD class="wig"><IMG class='toggle detail'> <div class="format"> <code>type wig <low#> <high#></code><BR> <code>type bigWig <#> <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="minLimit"> <A name="minLimit"></A> <A name="maxLimit"></A><IMG class='toggle detail'> <div class="format"> <code>type bedGraph <field></code><BR> <code>minLimit <#></code><BR> <code>maxLimit<#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="alwaysZero"><A name="alwaysZero"></A><IMG class='toggle detail'> <div class="format"><code>alwaysZero <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="autoScale"><A name="autoScale"></A><IMG class='toggle detail'> <div class="format"><code>autoScale <off/on/group></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="graphTypeDefault"> <A name="graphTypeDefault"></A><IMG class='toggle detail'> <div class="format"><code>graphTypeDefault points</code></div> </TD></TR> <TR VALIGN=TOP><TD class="logo"> <A name="logo"></A><IMG class='toggle detail'> <div class="format"><code>logo on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxHeightPixels"> <A name="maxHeightPixels"></A><IMG class='toggle detail'> <div class="format"><code>maxHeightPixels <max:default:min></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowToQuery"> <A name="maxWindowToQuery"></A><IMG class='toggle detail'> <div class="format"><code>maxWindowToQuery <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="negateValues"> <A name="negateValues"></A><IMG class='toggle detail'> <div class="format"><code>negateValues <on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="spanList"><A name="spanList"></A><IMG class='toggle detail'> <div class="format"><code>spanList <s1>[,s2…]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="smoothingWindow"> <A name="smoothingWindow"></A><IMG class='toggle detail'> <div class="format"><code>smoothingWindow <off/1-16></code></div> </TD></TR> <TR VALIGN=TOP><TD class="transformFunc"> <A name="transformFunc"></A><IMG class='toggle detail'> <div class="format"><code>transformFunc <NONE/LOG></code></div> </TD></TR> <TR VALIGN=TOP><TD class="mouseOverFunction"> <A name="mouseOverFunction"></A><IMG class='toggle detail'> <div class="format"><code>mouseOverFunction <noAverage></code></div> </TD></TR> <TR VALIGN=TOP><TD class="viewLimits"> <A name="viewLimits"></A> <A name="viewLimitsMax"></A><IMG class='toggle detail'> <div class="format"> <code>viewLimits <lower:upper></code><BR> <code>viewLimitsMax <lower:upper></code></div> </TD></TR> <TR VALIGN=TOP><TD class="wigColorBy"><A name="wigColorBy"></A><IMG class='toggle detail'> <div class="format"><code>wigColorBy <bedTable></code></div> </TD></TR> <TR VALIGN=TOP><TD class="windowingFunction"> <A name="windowingFunction"></A><IMG class='toggle detail'> <div class="format"><code>windowingFunction <mean/mean+whiskers/maximum/minimum></code></div> </TD></TR> <TR VALIGN=TOP><TD class="yLineMark"> <A name="yLineMark"></A> <A name="yLineOnOff"></A> <A name="gridDefault"></A><IMG class='toggle detail'> <div class="format"> <code>yLineMark <#></code><BR> <code>yLineOnOff <off/on></code><BR> <code>gridDefault on</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="wig_example"><IMG class='toggle detail'> <div class="format"><B>Examples of signal graphing tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="genePred"></A> <TABLE class="settingsTable" id="genePred_-_Gene_Model_Track_Settings"> <THEAD><TR><TD><DIV ID="genePred_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> genePred - Gene model track settings </TH></TR> <TR VALIGN=TOP><TD class="genePred"><IMG class='toggle detail'> <div class="format"><code>type genePred [pepTable [mrnaTable]]</code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="geneClasses"> <A name="geneClasses"></A><IMG class='toggle detail setC'> <div class="format"><I>Related settings:</I><BR> <code>geneClasses <cl1 cl2...></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="gClass_"> <A name="gClass_"></A><IMG class='toggle detail setC'> <div class="format"><code>gClass_<xxx> <red,green,blue></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="itemClassTbl"> <A name="itemClassTbl"></A><IMG class='toggle detail setC'> <div class="format"><code>itemClassTbl <table></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="itemClassNameColumn"> <A name="itemClassNameColumn"></A><IMG class='toggle detail setC'> <div class="format"><code>itemClassNameColumn <col></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="itemClassClassColumn"> <A name="itemClassClassColumn"></A><IMG class='toggle detail setC'> <div class="format"><code>itemClassClassColumn <col></code></div> </TD></TR> <TR VALIGN=TOP><TD class="filterBy_genePred"> <A name="filterBy_genePred"></A><IMG class='toggle detail'> <div class="format"><code>filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="autoTranslate"><A name="autoTranslate"></A><IMG class='toggle detail'> <div class="format"><code>autoTranslate 0</code></div> </TD></TR> <TR VALIGN=TOP><TD class="intronGap"><A name="intronGap"></A><IMG class='toggle detail'> <div class="format"><code>intronGap <#bases></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLinkedTables"> <A name="defaultLinkedTables"></A><IMG class='toggle detail'> <div class="format"><code>defaultLinkedTables <table1>[,table2...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="idXref"><A name="idXref"></A><IMG class='toggle detail'> <div class="format"><code>idXref <idColumn> <altIdColumn></code></div> </TD></TR> <TR VALIGN=TOP><TD class="oldToNew"><A name="oldToNew"></A><IMG class='toggle detail'> <div class="format"><code>oldToNew <tableName></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying gene models.</P> <A onclick="return jumpTo(this);" HREF="#">baseColorUseSequence</A>, <A onclick="return jumpTo(this);" HREF="#">baseColorDefault</A>, <A onclick="return jumpTo(this);" HREF="#">itemDetailsHtmlTable</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowCoverage</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesAllScales</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesMaxZoom</A> <A onclick="return jumpTo(this);" HREF="#">decorator</A> </TD></TR> <TR class="examples" VALIGN=TOP> <TD class="genePred_example"><IMG class='toggle detail'> <div class="format"><B>Examples of genePred tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="bam"></A> <TABLE class="settingsTable" id="bam_-_Compressed_Alignment_Track_Settings"> <THEAD><TR><TD><DIV ID="bam_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bam/cram - Compressed Sequence Alignment track settings</TH></TR> <TR VALIGN=TOP><TD class="bam"><IMG class='toggle detail'> <div class="format"><code>type bam</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataIndex"><A name="bigDataIndex"></A><IMG class='toggle detail'> <div class="format"><code>bigDataIndex <url/relativePath></code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="bamColorMode"> <A name="bamColorMode"></A><IMG class='toggle detail setD'> <div class="format"><I>Related settings:</I><BR> <code>bamColorMode <strand/gray/tag/off></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="bamGrayMode"> <A name="bamGrayMode"></A> <A name="aliQualRange"></A> <A name="baseQualRange"></A><IMG class='toggle detail setD'> <div class="format"> <code>bamGrayMode <aliQual/baseQual/unpaired></code><BR> <code>aliQualRange <min:max></code><BR> <code>baseQualRange <min:max></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="bamColorTag"> <A name="bamColorTag"></A><IMG class='toggle detail setD'> <div class="format"><code>bamColorTag <XX></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="noColorTag"> <A name="noColorTag"></A><IMG class='toggle detail setD'> <div class="format"><code>noColorTag .</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bamSkipPrintQualScore"><A name="bamSkipPrintQualScore"></A> <IMG class='toggle detail'> <div class="format"><code>bamSkipPrintQualScore .</code></div> </TD></TR> <TR VALIGN=TOP><TD class="indelDoubleInsert"> <A name="indelDoubleInsert"></A> <A name="indelQueryInsert"></A> <A name="indelPolyA"></A><IMG class='toggle detail'> <div class="format"> <code>indelDoubleInsert <off/on></code><BR> <code>indelQueryInsert <off/on></code><BR> <code>indelPolyA <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="minAliQual"><A name="minAliQual"></A><IMG class='toggle detail'> <div class="format"><code>minAliQual <#></code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="pairEndsByName"> <A name="pairEndsByName"></A><IMG class='toggle detail setE'> <div class="format"><I>Related settings:</I><BR> <code>pairEndsByName .</code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="pairSearchRange"> <A name="pairSearchRange"></A><IMG class='toggle detail setE'> <div class="format"><code>pairSearchRange <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showNames"><A name="showNames"></A><IMG class='toggle detail'> <div class="format"><code>showNames <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="doWiggle"><A name="doWiggle"></A><IMG class='toggle detail'> <div class="format"><code>doWiggle on</code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying bam tags.</P> <A onclick="return jumpTo(this);" HREF="#">baseColorUseSequence</A>, <A onclick="return jumpTo(this);" HREF="#">baseColorDefault</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowCoverage</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesAllScales</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesMaxZoom</A> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bam_example"><IMG class='toggle detail'> <div class="format"><B>Example for bam track:</B></div> </TD></TR> </TABLE> <BR><BR> <a name="bigBarChart"></a> <style> .dot { display: inline-block; height: 10px; width: 10px; margin-right: 2px; border-radius: 50%; } </style> <table class="settingsTable" id="bigBarChart"> <thead><tr><td><div ID="bigBarChart_intro" class="intro"></div></td></tr></thead> <tr valign=top><th><img class='toggle oneSection'> bigBarChart - Bar chart display of categorical variables over genomic regions </th></tr> <tr valign=top><td class="bigBarChart"><img class='toggle detail'> <div class="format"> <code>type bigBarChart</code></div> </td></tr> <tr valign=top><td class="barChartBars"><a name="barChartBars"></a><img class='toggle detail'> <div class="format"> <code class="level-required">barChartBars <label1 label2...></code></div> </td></tr> <tr valign=top><td class="bigDataUrl"><img class='toggle detail'> <div class="format"><code class="level-required">bigDataUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="barChartColors"><a name="barChartColors"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">barChartColors <color1 color2...></code> </div> <tr valign=top><td class="barChartLabel"><a name="barChartLabel"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">barChartLabel <label></code> </div> <tr valign=top><td class="barChartMaxSize"><a name="barChartMaxSize"></a> <img class='toggle detail'> <div class="format"><code class="level-full">barChartMaxSize <small/medium/large></code> </div> </td></tr> <tr valign=top><td class="barChartSizeWindows"><a name="barChartSizeWindows"></a> <img class='toggle detail'> <div class="format"><code class="level-new"> barChartSizeWindows <largeMax> <smallMin></code> </div> <tr valign=top><td class="barChartStretchToItem"><a name="barChartStretchToItem"></a> <img class='toggle detail'> <div class="format"><code class="level-new"> barChartStretchToItem on</code> </div> </td></tr> <tr valign=top><td class="barChartMetric"><a name="barChartMetric"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">barChartMetric <metric></code> </div> <tr valign=top><td class="barChartUnit"><a name="barChartUnit"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">barChartUnit <unit></code> </div> <tr valign=top><td class="barChartMatrixUrl"><a name="barChartMatrixUrl"></a> <img class='toggle detail'> <div class="format"><code class="level-full">barChartMatrixUrl <url/relativePath></code> </div> <tr valign=top><td class="barChartSampleUrl"><a name="barChartSampleUrl"></a> <img class='toggle detail'> <div class="format"><code class="level-full">barChartSampleUrl <url/relativePath></code> </div> <tr valign=top><td class="barChartCategoryUrl"><a name="barChartCategoryUrl"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartCategoryUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="barChartFacets"><a name="barChartFacets"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartFacets <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="barChartStatsUrl"><a name="barChartStatsUrl"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartStatsUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="barChartStatsUrl"><a name="barChartMerge"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartMerge <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="barChartBarMinPadding"><a name="barChartBarMinPadding"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartBarMinPadding <num></code> </div> </td></tr> <tr valign=top><td class="barChartBarMinWidth"><a name="barChartBarMinWidth"></a> <img class='toggle detail'> <div class="format"><code class="level-new">barChartBarMinWidth <num></code> </div> </td></tr> <tr valign=top><td class="maxLimit"><img class='toggle detail'> <div class="format"><code class="level-full">maxLimit <maximum-bar-value></code> </div> <tr valign=top><td> <p>Additional settings defined in other sections are also available for displaying bigBarChart tracks.</p> <a onclick="return jumpTo(this);" HREF="#">labelFields</a>, <a onclick="return jumpTo(this);" HREF="#">defaultLabelFields</a> <a onclick="return jumpTo(this);" HREF="#">url</a> <a onclick="return jumpTo(this);" HREF="#">urlLabel</a> <a onclick="return jumpTo(this);" HREF="#">urls</a> </td></tr> <tr class="examples" valign=top><td class="bigBarChart_example"><img class='toggle detail'> <div class="format"><b>Example of a bigBarChart track</b></div> </td></tr> </table> <br><br> <a name="bigInteract"></a> <table class="settingsTable" id="bigInteract"> <thead><tr><td><div ID="bigInteract_intro" class="intro"></div></td></tr></thead> <tr valign=top><th><img class='toggle oneSection'> bigInteract - Pairwise interaction display </th></tr> <tr valign=top><td class="bigInteract"><img class='toggle detail'> <div class="format"> <code>type bigInteract</code></div> </td></tr> <tr valign=top><td class="bigDataUrl"><img class='toggle detail'> <div class="format"><code class="level-required">bigDataUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="interactDirectional"><a name="interactDirectional"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">interactDirectional <true/offsetSource/offsetTarget/clusterSource/clusterTarget></code> </div> </td></tr> <tr valign=top><td class="interactUp"><a name="interactUp"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">interactUp <true/false></code> </div> </td></tr> <tr valign=top><td class="detailsBoxesEnabled"><a name="detailsBoxesEnabled"></a> <img class='toggle detail'> <div class="format"> <code class="level-new">detailsBoxesEnabled <true/false></code> </div> </td></tr> <tr valign=top><td class="interactMultiRegion"><a name="interactMultiRegion"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">interactMultiRegion <true/padding></code> </div> </td></tr> <tr valign=top><td> <p>Additional settings defined in other sections are also available for displaying bigInteract tracks.</p> <a onclick="return jumpTo(this);" HREF="#">maxHeightPixels</a> <a onclick="return jumpTo(this);" HREF="#">scoreMin</a> <a onclick="return jumpTo(this);" HREF="#">spectrum</a>, </td></tr> <tr class="examples" valign=top><td class="interact_example"><img class='toggle detail'> <div class="format"><b>Example of a bigInteract track</b></div> </td></tr> </table> <br><br> <a name="bigLolly"></a> <table class="settingsTable" id="bigLolly"> <thead><tr><td><div ID="bigLolly_intro" class="intro"></div></td></tr></thead> <tr valign=top><th><img class='toggle oneSection'> bigLolly - Lollipop charts </th></tr> <tr valign=top><td class="bigLolly"><img class='toggle detail'> <div class="format"> <code>type bigLolly</code></div> </td></tr> <tr valign=top><td class="bigDataUrl"><img class='toggle detail'> <div class="format"><code class="level-required">bigDataUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="noStems"><img class='toggle detail'> <div class="format"><code class="level-required">noStems <on/off></code> </div> </td></tr> <tr valign=top><td class="lollySizeField"><img class='toggle detail'> <div class="format"><code class="level-required">lollySizeField <integer></code> </div> </td></tr> <tr valign=top><td class="lollyMaxSize"><img class='toggle detail'> <div class="format"><code class="level-required">lollyMaxSize <integer></code> </div> </td></tr> <tr valign=top><td class="lollyField"><img class='toggle detail'> <div class="format"><code class="level-required">lollyField <integer></code> </div> </td></tr> <tr valign=top><td class="yAxisLabel"><img class='toggle detail'> <div class="format"><code class="level-full"><code>yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string> </code></div> </td></tr> <tr valign=top><td class="yAxisNumLabels"><img class='toggle detail'> <div class="format"><code class="level-required">yAxisNumLabels <on/off></code> </div> </td></tr> <tr class="examples" valign=top><td class="bigLolly_example"><img class='toggle detail'> <div class="format"><b>Example of a bigLolly track</b></div> </td></tr> </table> <br><br> <a name="hic"></a> <table class="settingsTable" id="hic"> <thead><tr><td><div ID="hic_intro" class="intro"></div></td></tr></thead> <tr valign=top><th><img class='toggle oneSection'> hic - Hi-C contact matrices </th></tr> <tr valign=top><td class="hic"><img class='toggle detail'> <div class="format"> <code>type hic</code></div> </td></tr> <tr valign=top><td class="bigDataUrl"><img class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code> </div> </td></tr> <tr valign=top><td class="color"><img class='toggle detail'> <div class="format"><code>color <red,green,blue></code> </div> </td></tr> <tr valign=top><td class="drawMode"><a name="drawMode"></a><img class='toggle detail'> <div class="format"><code>drawMode <triangle|square|arc></code> </div> </td></tr> <tr valign=top><td class="normalization"><a name="normalization"></a><img class='toggle detail'> <div class="format"><code>normalization <NONE|VC|VC_SQRT|KR></code> </div> </td></tr> <tr valign=top><td class="resolution"><a name="resolution"></a><img class='toggle detail'> <div class="format"><code>resolution <Auto|integer></code> </div> </td></tr> <tr valign=top><td class="saturationScore"><a name="saturationScore"></a><img class='toggle detail'> <div class="format"><code>saturationScore <float></code> </div> </td></tr> <tr valign=top><td class="autoScale"><a name="autoScale"></a><img class='toggle detail'> <div class="format"><code>autoScale <off/on/group></code> </div> </td></tr> <tr valign=top><td class="hicDistanceMin"><a name="hicDistanceMin"></a><img class='toggle detail'> <div class="format"><code>hicDistanceMin <integer></code> </div> </td></tr> <tr valign=top><td class="hicDistanceMax"><a name="hicDistanceMax"></a><img class='toggle detail'> <div class="format"><code>hicDistanceMax <integer></code> </div> </td></tr> +<tr valign=top><td class="hicArcLimit"><a name="hicArcLimit"></a><img class='toggle detail'> + <div class="format"><code>hicArcLimit <integer></code> + </div> +</td></tr> +<tr valign=top><td class="hicArcLimitEnabled"><a name="hicArcLimitEnabled"></a><img class='toggle detail'> + <div class="format"><code>hicArcLimitEnabled <true|false></code> + </div> +</td></tr> <tr class="examples" valign=top><td class="hic_example"><img class='toggle detail'> <div class="format"><b>Example of a hic track</b></div> </td></tr> </table> <br><br> <A name="pgSnp"></A> <TABLE class="settingsTable" id="pgSnp_-_Personal_Genome_SNP_Track_Settings"> <THEAD><TR><TD><DIV ID="pgSnp_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> pgSnp - Personal Genome SNP track settings </TH></TR> <TR VALIGN=TOP><TD class="pgSnp"><IMG class='toggle detail'> <div class="format"><code>type pgSnp</code></div> </TD></TR> <TR VALIGN=TOP><TD class="pgPolyphenPredTab"><A name="pgPolyphenPredTab"></A><IMG class='toggle detail'> <div class="format"><code>pgPolyphenPredTab <arg></code></div> </TD></TR> <TR VALIGN=TOP><TD class="pgSiftPredTab"><A name="pgSiftPredTab"></A><IMG class='toggle detail'> <div class="format"><code>pgSiftPredTab <arg></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="pgSnp_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a Personal Genome SNP track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="vcfTabix"></A> <TABLE class="settingsTable" id="vcfTabix_-_Variant_Call_Format_Track_Settings"> <THEAD><TR><TD><DIV ID="vcfTabix_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'/> vcfTabix - Variant Call Format (indexed by tabix) track settings </TH></TR> <TR VALIGN=TOP><TD class="vcfTabix"><IMG class='toggle detail'> <div class="format"><code>type vcfTabix</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code>bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataIndex"><A name="bigDataIndex"></A><IMG class='toggle detail'> <div class="format"><code>bigDataIndex <url/relativePath></code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="hapClusterEnabled"><A NAME="hapClusterEnabled"><IMG class='toggle detail setF'> <div class="format"><I>Related settings:</I><BR> <code>hapClusterEnabled <true|false></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="hapClusterMethod"><A NAME="hapClusterMethod"><IMG class='toggle detail setF'> <div class="format"><code class="level-full">hapClusterMethod <centerWeighted|fileOrder|treeFile <em>url</em>></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="hapClusterColorBy"><A NAME="hapClusterColorBy"><IMG class='toggle detail setF'> <div class="format"><code class="level-full"><code>hapClusterColorBy <altOnly|function|refAlt|base></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="geneTrack"><A NAME="geneTrack"><IMG class='toggle detail setF'> <div class="format"><code class="level-new">geneTrack <<em>track</em>></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="hapClusterTreeAngle"><A NAME="hapClusterTreeAngle"><IMG class='toggle detail setF'> <div class="format"><code>hapClusterTreeAngle <triangle|rectangle></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="hapClusterHeight"><A NAME="hapClusterHeight"><IMG class='toggle detail setF'> <div class="format"><code>hapClusterHeight <N></code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="applyMinQual"><A NAME="applyMinQual"><IMG class='toggle detail setG'> <div class="format"><I>Related settings:</I><BR> <code>applyMinQual <true|false></code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="minQual"><A NAME="minQual"><IMG class='toggle detail setG'> <div class="format"><code>minQual <<EM>Q</EM>></code></div> </TD></TR> <TR VALIGN=TOP><TD class="minFreq"><A NAME="minFreq"><IMG class='toggle detail'> <div class="format"><code>minFreq <<EM>F</EM>></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoFilter"><A NAME="vcfDoFilter"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoFilter <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoQual"><A NAME="vcfDoQual"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoMaf"><A NAME="vcfDoQual"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks.</P> <A onclick="return jumpTo(this);" HREF="#">maxWindowCoverage</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A> </DIV> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="vcfTabix_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a VCF track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="vcfPhasedTrio"></A> <TABLE class="settingsTable" id="vcfPhasedTrio_-_Variant_Call_Format_Track_Settings"> <THEAD><TR><TD><DIV ID="vcfPhasedTrio_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'/> vcfPhasedTrio - Variant Call Format Trio track settings </TH></TR> <TR VALIGN=TOP><TD class="vcfPhasedTrio"><IMG class='toggle detail'> <div class="format"><code>type vcfPhasedTrio</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfChildSample"><IMG class='toggle detail'> <div class="format"><code class="level-required">vcfChildSample <sampleName|altName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataIndex"><IMG class='toggle detail'> <div class="format"><code class="level-full">bigDataIndex <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfParentSamples"><A NAME="vcfParentSamples"><IMG class='toggle detail'> <div class="format"><code class="level-full">vcfParentSamples <sampleName|altName,sampleName|altName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfUseAltSampleNames"><A NAME="vcfUseAltSampleNames"><IMG class='toggle detail'> <div class="format"><code class="level-full">vcfUseAltSampleNames <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="geneTrack"><A NAME="geneTrack"><IMG class='toggle detail'> <div class="format"><code class="level-new">geneTrack <track></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoFilter"><A NAME="vcfDoFilter"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoFilter <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoQual"><A NAME="vcfDoQual"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoMaf"><A NAME="vcfDoQual"><IMG class='toggle detail'> <div class="format"><code class="level-new">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks.</P> <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A> </DIV> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="vcfPhasedTrio_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a VCF Phased Trio track</B></div> </TD></TR> </TABLE> <BR><BR> <A name="psl"></A> <TABLE class="settingsTable" id="psl_-_Sequence_Alignment_Track_Settings"> <THEAD><TR><TD><DIV ID="psl_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> psl - Sequence alignment tracks settings </TH></TR> <TR VALIGN=TOP><TD class="psl"><IMG class='toggle detail'> <div class="format"><code>type psl <subtype> [otherDb]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="blastRef"><A name="blastRef"></A><IMG class='toggle detail'> <div class="format"><code>blastRef <assembly.table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="colorChromDefault"> <A name="colorChromDefault"></A><IMG class='toggle detail'> <div class="format"><code>colorChromDefault off</code></div> </TD></TR> <TR VALIGN=TOP><TD class="pred"><A name="pred"></A><IMG class='toggle detail'> <div class="format"><code>pred <assembly.table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="pslSequence"><A name="pslSequence"></A><IMG class='toggle detail'> <div class="format"><code>pslSequence <no/all/different></code></div> </TD></TR> <TR VALIGN=TOP><TD class="transMapGene"> <A name="transMapGene"></A> <A name="transMapInfo"></A> <A name="transMapSrc"></A> <A name="transMapTypeDesc"></A><IMG class='toggle detail'> <div class="format"> <code>transMapGene <assembly.table></code><BR> <code>transMapInfo <table></code><BR> <code>transMapSrc <assembly.table></code><BR> <code>transMapTypeDesc <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="ucscRetroInfo"><A name="ucscRetroInfo"></A><IMG class='toggle detail'> <div class="format"><code>ucscRetroInfo</code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings defined elsewhere in this document are also available for displaying psl tracks.</P> <A onclick="return jumpTo(this);" HREF="#">baseColorUseSequence</A>, <A onclick="return jumpTo(this);" HREF="#">baseColorDefault</A>, <A onclick="return jumpTo(this);" HREF="#">chainLinearGap</A>, <A onclick="return jumpTo(this);" HREF="#">chainMinScore</A>, <A onclick="return jumpTo(this);" HREF="#">indelDoubleInsert</A>, <A onclick="return jumpTo(this);" HREF="#">indelQueryInsert</A>, <A onclick="return jumpTo(this);" HREF="#">indelPolyA</A>, <A onclick="return jumpTo(this);" HREF="#">itemDetailsHtmlTable</A>, <A onclick="return jumpTo(this);" HREF="#">matrix</A>, <A onclick="return jumpTo(this);" HREF="#">matrixHeader</A>, <A onclick="return jumpTo(this);" HREF="#">maxItems</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowCoverage</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, <A onclick="return jumpTo(this);" HREF="#">showCdsAllScales</A>, <A onclick="return jumpTo(this);" HREF="#">showCdsMaxZoom</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesAllScales</A>, <A onclick="return jumpTo(this);" HREF="#">showDiffBasesMaxZoom</A>, <A onclick="return jumpTo(this);" HREF="#">spectrum</A> <A onclick="return jumpTo(this);" HREF="#">decorator</A> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="psl_example"><IMG class='toggle detail'> <div class="format"><B>Examples of psl alignment tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="chain"><A name="netAlign"></A> <TABLE class="settingsTable" id="chain_netAlign_-_Paired_Alignment_Track_Settings"> <THEAD><TR><TD><DIV ID="chain_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> chain and netAlign - paired species alignment track settings </TH></TR> <TR VALIGN=TOP><TD class="chain"><IMG class='toggle detail'> <div class="format"> <code>type chain <otherDb></code><BR> <code>otherDb <otherDb></code></div> </TD></TR> <TR VALIGN=TOP><TD class="netAlign"><IMG class='toggle detail'> <div class="format"> <code>type netAlign <otherDb> <otherChainTable></code><BR> <code>otherDb <otherDb></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chainColor"><A name="chainColor"></A><IMG class='toggle detail'> <div class="format"><code>chainColor <scheme></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chainLinearGap"> <A name="chainLinearGap"></A><IMG class='toggle detail'> <div class="format"><code>chainLinearGap <loose/medium></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chainMinScore"><A name="chainMinScore"></A><IMG class='toggle detail'> <div class="format"><code>chainMinScore <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chainNormScoreAvailable"> <A name="chainNormScoreAvailable"></A><IMG class='toggle detail'> <div class="format"><code>chainNormScoreAvailable <yes/no></code></div> </TD></TR> <TR VALIGN=TOP><TD class="matrix"> <A name="matrix"></A> <A name="matrixHeader"></A><IMG class='toggle detail'> <div class="format"> <code>matrix <size> <#,#,#,#,…></code><BR> <code>matrixHeader <b1,b2,b3,b4></code><BR> <code>$matrix</code> token in html.</div> </DIV> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"></A><IMG class='toggle detail'> <div class="format"><code>otherTwoBitUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="spectrum"><IMG class='toggle detail'> <div class="format"><code>spectrum on</code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="baseColorDefault"> <A name="baseColorDefault"></A><IMG class='toggle detail setB'> <div class="format"><code>baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> <TR VALIGN=TOP><TD class="indelDoubleInsert"> <A name="indelDoubleInsert"></A> <A name="indelQueryInsert"></A> <A name="indelPolyA"></A><IMG class='toggle detail'> <div class="format"> <code>indelDoubleInsert <off/on></code><BR> <code>indelQueryInsert <off/on></code><BR> <code>indelPolyA <off/on></code></div> </TD></TR> <!-- <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying chains and netAligns.</P> <A onclick="return jumpTo(this);" HREF="#">spectrum</A> </TD></TR> --> <TR class="examples" VALIGN=TOP><TD class="chain_netAlign_example"> <IMG class='toggle detail'> <div class="format"><B>Examples of chain and netAlign tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="wigMaf"></A> <TABLE class="settingsTable" id="wigMaf_-_Multiple_Alignment_Track_Settings"> <THEAD><TR><TD><DIV ID="wigMaf_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> wigMaf - Multiple alignment track settings </TH></TR> <TR VALIGN=TOP><TD class="wigMaf"><IMG class='toggle detail'> <div class="format"><code>type wigMaf <minVal> <maxVal></code></div> </TD></TR> <TR VALIGN=TOP><TD class="frames"><A name="frames"></A><IMG class='toggle detail'> <div class="format"><code>frames <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="irows"><A name="irows"></A><IMG class='toggle detail'> <div class="format"><code>irows off</code></div> </TD></TR> <TR VALIGN=TOP><TD class="itemFirstCharCase"> <A name="itemFirstCharCase"></A><IMG class='toggle detail'> <div class="format"><code>itemFirstCharCase noChange</code></div> </TD></TR> <TR VALIGN=TOP><TD class="pairwiseHeight"> <A name="pairwiseHeight"></A><IMG class='toggle detail'> <div class="format"><code>pairwiseHeight <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="speciesCodonDefault"> <A name="speciesCodonDefault"></A><IMG class='toggle detail'> <div class="format"><code>speciesCodonDefault <species></code></div> </TD></TR> <TR VALIGN=TOP><TD class="speciesDefaultOff"> <A name="speciesDefaultOff"></A><IMG class='toggle detail'> <div class="format"><code>speciesDefaultOff <species1> [species2 ...]</code></div> </TD></TR> <TR class="related1st" VALIGN=TOP><TD class="speciesOrder"> <A name="speciesOrder"></A><IMG class='toggle detail setF'> <div class="format"><I>Related settings:</I><BR> <code>speciesOrder <species1> [species2 …]</code></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="speciesGroups"> <A name="speciesGroups"></A> <A name="sGroup_"></A><IMG class='toggle detail setF'> <div class="format"> <code>speciesGroups <sgroup1> [sgroup2 …]</code><BR> <code>sGroup_<sgroupN> <species1> [species2 …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="speciesLabels"><A name="speciesLabels"></A><IMG class='toggle detail'> <div class="format"><code>speciesLabels <species1=newLabel1> [species2=newLabel2 …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="summary"><A name="summary"></A><IMG class='toggle detail'> <div class="format"><code>summary <tableName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="treeImage"><A name="treeImage"></A><IMG class='toggle detail'> <div class="format"><code>treeImage <imageFile></code></div> </TD></TR> <TR VALIGN=TOP><TD class="wiggle"><A name="wiggle"></A><IMG class='toggle detail'> <div class="format"><code>wiggle <table1> <leftLabel1> <uiLabel1> [table2 leftLabel2 uiLabelN ...]</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="wigMaf_example"> <IMG class='toggle detail'> <div class="format"><B>Examples of wigMaf tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="expRatio"></A> <TABLE class="settingsTable" id="expRatio_-_Microarray_Expression_Track_Settings"> <THEAD><TR><TD><DIV ID="expRatio_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> expRatio - Microarray expression track settings </TH></TR> <TR VALIGN=TOP><TD class="expRatio"><IMG class='toggle detail'> <div class="format"><code>type expRatio</code></div> </TD></TR> <TR VALIGN=TOP><TD class="expDrawExons"><A name="expDrawExons"></A><IMG class='toggle detail'> <div class="format"><code>expDrawExons on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="expScale"><A name="expScale"></A><IMG class='toggle detail'> <div class="format"><code>expScale <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="expStep"><A name="expStep"></A><IMG class='toggle detail'> <div class="format"><code>expStep <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="expTable"><A name="expTable"></A><IMG class='toggle detail'> <div class="format"><code>expTable <tableName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="groupings"><A name="groupings"></A><IMG class='toggle detail'> <div class="format"><code>groupings <fileName></code></div> </TD></TR> <TR class="examples" VALIGN=TOP> <TD class="expRatio_example"><IMG class='toggle detail'> <div class="format"><B>Example of an expRatio track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="snp"></A> <TABLE class="settingsTable" id="snp_-_short_genetic_variants_from_dbSNP_Track_Settings"> <THEAD><TR><TD><DIV ID="snp_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'/> snp - Short genetic variants from dbSNP track settings </TH></TR> <TR VALIGN=TOP><TD class="snp"><IMG class='toggle detail'> <div class="format"><code>type bed 6 +</code></div> </TD></TR> <TR VALIGN=TOP><TD class="chimpDb"><A name="chimpDb"></A><IMG class='toggle detail'> <div class="format"><code>chimpDb <db></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chimpMacaqueOrthoTable"><A name="chimpMacaqueOrthoTable"></A><IMG class='toggle detail'> <div class="format"><code>chimpMacaqueOrthoTable <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chimpOrangMacOrthoTable"><A name="chimpOrangMacOrthoTable"></A><IMG class='toggle detail'> <div class="format"><code>chimpOrangMacOrthoTable <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="codingAnnoLabel_table"><A name="codingAnnoLabel_table"></A><IMG class='toggle detail'> <div class="format"><code>codingAnnoLabel_<table> <text></code></div> </TD></TR> <TR VALIGN=TOP><TD class="codingAnnotations"><A name="codingAnnotations"></A><IMG class='toggle detail'> <div class="format"><code>codingAnnotations <table>[,table]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultGeneTracks"><A name="defaultGeneTracks"></A><IMG class='toggle detail'> <div class="format"><code>defaultGeneTracks <genesTrack>[,genesTrack]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultMaxWeight"><A name="defaultMaxWeight"></A><IMG class='toggle detail'> <div class="format"><code>defaultMaxWeight <1|2|3></code></div> </TD></TR> <TR VALIGN=TOP><TD class="hapmapPhase"><A name="hapmapPhase"></A><IMG class='toggle detail'> <div class="format"><code>hapmapPhase <II|III></code></div> </TR> <TR VALIGN=TOP><TD class="macaqueDb"><A name="macaqueDb"></A><IMG class='toggle detail'> <div class="format"><code>macaqueDb <db></code></div> </TD></TR> <TR VALIGN=TOP><TD class="orangDb"><A name="orangDb"></A><IMG class='toggle detail'> <div class="format"><code>orangDb <db></code></div> </TD></TR> <TR VALIGN=TOP><TD class="snpExceptions"><A name="snpExceptions"></A><IMG class='toggle detail'> <div class="format"><code>snpExceptions <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="snpExceptionDesc"><A name="snpExceptionDesc"></A><IMG class='toggle detail'> <div class="format"><code>snpExceptionDesc <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="snpSeq"><A name="snpSeq"></A><IMG class='toggle detail'> <div class="format"><code>snpSeq <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="snpSeqFile"><A name="snpSeqFile"></A><IMG class='toggle detail'> <div class="format"><code>snpSeqFile <path></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying snp tracks.</P> <A onclick="return jumpTo(this);" HREF="#">maxWindowCoverage</A> <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A> </DIV> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="snp_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a snp track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="rareTypes"></A> <H2 class="leftAlign">Specialized or rarely used types:</H2> <P><I>NONE OF THESE ARE FOR HUBS. Nor are any of their settings.</I></P> <A name="altGraphX"></A> <TABLE class="settingsTable" id="altGraphX_-_Alternate_Splicing_Track_Settings"> <THEAD><TR><TD><DIV ID="altGraphX_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> altGraphX - Alternate splicing gene model track settings </TH></TR> <TR VALIGN=TOP><TD class="altGraphX"><IMG class='toggle detail'> <div class="format"><code>type altGraphX</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="altGraphX_example"> <IMG class='toggle detail'> <div class="format"><B>Example of an altGraphX track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="bedDetail"></A> <TABLE class="settingsTable" id="bedDetail_-_Text_Extended_BED_Track_Settings"> <THEAD><TR><TD><DIV ID="bedDetail_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bedDetail - Text extended bed track settings </TH></TR> <TR VALIGN=TOP><TD class="bedDetail"><IMG class='toggle detail'> <div class="format"><code>type bedDetail <#></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings defined elsewhere in this document are also available for displaying bedDetail tracks.</P> <A onclick="return jumpTo(this);" HREF="#">itemRgb</A>, <A onclick="return jumpTo(this);" HREF="#">url</A>, <A onclick="return jumpTo(this);" HREF="#">urlLabel</A> <P><I>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.</I></P> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bedDetail_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a bedDetail track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="clonePos"></A> <TABLE class="settingsTable" id="clonePos_-_Genome_Coverage_Track_Settings"> <THEAD><TR><TD><DIV ID="clonePos_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> clonePos - Genome coverage track settings </TH></TR> <TR VALIGN=TOP><TD class="clonePos"><IMG class='toggle detail'> <div class="format"><code>type clonePos</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="clonePos_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a clonePos track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="ctgPos"></A> <TABLE class="settingsTable" id="ctgPos_-_Physical_Map_Contig_Track_Settings"> <THEAD><TR><TD><DIV ID="ctgPos_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> ctgPos - Physical map contigs track settings </TH></TR> <TR VALIGN=TOP><TD class="ctgPos"><IMG class='toggle detail'> <div class="format"><code>type ctgPos</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="ctgPos_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a ctgPos track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="downloadsOnly"></A> <TABLE class="settingsTable" id="downloadsOnly_Track_Settings"> <THEAD><TR><TD><DIV ID="downloadsOnly_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> downloadsOnly - Specialized downloadable file track settings </TH></TR> <TR VALIGN=TOP><TD class="downloadsOnly"><IMG class='toggle detail'> <div class="format"><code>type downloadsOnly</code></div> </TD></TR> <TR VALIGN=TOP><TD class="fileSortOrder_downloadsOnly"> <A name="fileSortOrder_downloadsOnly"></A><IMG class='toggle detail'> <div class="format"><code>fileSortOrder ...</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="downloadsOnly_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a Downloads Only track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="encodeFiveC"></A> <TABLE class="settingsTable" id="encodeFiveC_-_Five_C_Chromatin_Interaction_Track_Settings"> <THEAD><TR><TD><DIV ID="encodeFiveC_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> encodeFiveC - Five C Chromatin interaction track settings </TH></TR> <TR VALIGN=TOP><TD class="encodeFiveC"><IMG class='toggle detail'> <div class="format"><code>type encodeFiveC</code></div> </TD></TR> <TR VALIGN=TOP><TD class="interTable"><A name="interTable"></A><IMG class='toggle detail'> <div class="format"><code>interTable <tableName></code></div> </TD></TR> <TR VALIGN=TOP><TD class="interTableKind"> <A name="interTableKind"></A><IMG class='toggle detail'> <div class="format"><code>interTableKind <label></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="encodeFiveC_example"> <IMG class='toggle detail'> <div class="format"><B>Example of an encodeFiveC track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="factorSource"></A> <TABLE class="settingsTable" id="factorSource_-_Combined_Item_Track_Settings"> <THEAD><TR><TD><DIV ID="factorSource_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> factorSource - Combined items track settings </TH></TR> <TR VALIGN=TOP><TD class="factorSource"><IMG class='toggle detail'> <div class="format"><code>type factorSource</code></div> </TD></TR> <TR VALIGN=TOP><TD class="sourceTable"><A name="sourceTable"></A><IMG class='toggle detail'> <div class="format"><code>sourceTable <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="inputTrackTable"> <A name="inputTrackTable"></A><IMG class='toggle detail'> <div class="format"><code>inputTrackTable <table></code></div> </TD></TR> <TR VALIGN=TOP><TD class="inputTableFieldDisplay"> <A name="inputTableFieldDisplay"></A><IMG class='toggle detail'> <div class="format"><code>inputTableFieldDisplay <f1> [f2...]</code></div> <TR VALIGN=TOP><TD class="filterBy_factorSource"> <A name="filterBy_factorSource"></A><IMG class='toggle detail'> <div class="format"><code>filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="motifDrawDefault"> <A name="motifDrawDefault"></A><IMG class='toggle detail'> <div class="format"><code>motifTable <on></code></div> <TR VALIGN=TOP><TD class="motifTable"> <A name="motifTable"></A><IMG class='toggle detail'> <div class="format"><code>motifTable <table></code></div> <TR VALIGN=TOP><TD class="motifPwmTable"> <A name="motifPwmTable"></A><IMG class='toggle detail'> <div class="format"><code>motifPwmTable <table></code></div> <TR VALIGN=TOP><TD class="motifMapTable"> <A name="motifMapTable"></A><IMG class='toggle detail'> <div class="format"><code>motifMapTable <table></code></div> <TR VALIGN=TOP><TD class="motifMaxWindow"> <A name="motifMaxWindow"></A><IMG class='toggle detail'> <div class="format"><code>motifMaxWindow <window size></code></div> <TR class="examples" VALIGN=TOP><TD class="factorSource_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a factorSource track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="rmsk"></A> <TABLE class="settingsTable" id="rmsk_-_Repeat_Masking_Track_Settings"> <THEAD><TR><TD><DIV ID="rmsk_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> rmsk - Repeat masking track settings </TH></TR> <TR VALIGN=TOP><TD class="rmsk"><IMG class='toggle detail'> <div class="format"><code>type rmsk</code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying gene models.</P> <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, <A onclick="return jumpTo(this);" HREF="#">spectrum</A> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="rmsk_example"><IMG class='toggle detail'> <div class="format"><B>Example of a Repeat Masking track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="snake"></A> <TABLE class="settingsTable" id="snake_-_Self_Referencing_Alignment_Track_Settings"> <THEAD><TR><TD><DIV ID="snake_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> snake - Self referencing alignment track settings </TH></TR> <TR VALIGN=TOP><TD class="snake"><IMG class='toggle detail'> <div class="format"> <code>type snake <db></code><BR> <code>otherDb <otherDb></code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>Additional settings found in the "Item or region tracks" section are also available for displaying snake tracks.</P> <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, <A onclick="return jumpTo(this);" HREF="#">spectrum</A> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="snake_example"><IMG class='toggle detail'> <div class="format"><B>Example of a snake track:</B></div> </TD></TR> </TABLE> </div></div> <!-- Next section --> <div class="contentBorder"> <A name="groupingTracks"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Grouping tracks into sets and hierarchies</div> </div> <div class="borderGuard"> <P>All tracks have to be assigned to one predefined track group ("Mapping and sequencing", "Genes", etc).<br> In addition and depending on how closely related they are, tracks can be organized into one of three hierarchical containers: <ul> <li>"<A href="#multiWig">multiWig</A>" container: when the tracks are all in signal (wiggle or bigWig) format and it makes sense to overlay them.<br> Example: a set of bigWig tracks with H3K27ac signal, all on the same scale</li> <li>"<A href="#compositeTrack">composite</A>" container: when the tracks are expected to be configured together or have an internal subgrouping, like cell type or cell treatment.<br> Example: a set of ChIP-bigBeds in three different cell types</li> <li>"<A href="#superTrack">superTrack</A>" container: when the tracks share no specific configuration and you mostly want to show them together.<br> Example: a set of composite tracks or a mix of bigBed, bigWig and bam</li> </ul> <A name="group"></A> <TABLE class="settingsTable" id="Predefined_Group_Setting"> <THEAD><TR><TD><DIV ID="group_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Predefined major track groupings setting </TH></TR> <TR VALIGN=TOP><TD class="group"><IMG class='toggle detail'> <div class="format"><code>group <groupId></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="group_example"><IMG class='toggle detail'> <div class="format"><B>Example of a track belonging to a predefined group:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="superTrack"></A> <TABLE class="settingsTable" id="superTrack_-_Folder_Track_Settings"> <THEAD><TR><TD><DIV ID="superTrack_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Supertrack (Folders) track settings </TH></TR> <TR VALIGN=TOP><TD class="superTrack"><IMG class='toggle detail'> <div class="format"><code>superTrack on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="parent_supertrack"> <A name="parent_supertrack"></A><IMG class='toggle detail'> <div class="format"><code>parent <superTrack></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="superTrack_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a Supertrack:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="compositeTrack"></A> <TABLE class="settingsTable" id="Composite_Track_Settings"> <THEAD><TR><TD><DIV ID="compositeTrack_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Composite track settings</TH></TR> <TR VALIGN=TOP><TD class="compositeTrack"><IMG class='toggle detail'> <div class="format"><code>compositeTrack on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="parent"><A name="parent"></A><IMG class='toggle detail'> <div class="format"><code>parent <composite> [off/on]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="allButtonPair"><A name="allButtonPair"></A><IMG class='toggle detail'> <div class="format"><code>allButtonPair on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="centerLabelsDense"> <A name="centerLabelsDense"></A><IMG class='toggle detail'> <div class="format"><code>centerLabelsDense <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="dragAndDrop"><A name="dragAndDrop"></A><IMG class='toggle detail'> <div class="format"><code>dragAndDrop subTracks</code></div> </TD></TR> <TR VALIGN=TOP><TD class="hideEmptySubtracks"><A name="hideEmptySubtracks"></A> <IMG class='toggle detail'> <div class="format"> <code>hideEmptySubtracks <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="hideEmptySubtracksMultiBedUrl"><A name="hideEmptySubtracksMultiBedUrl"></A> <IMG class='toggle detail'> <div class="format"> <code>hideEmptySubtracksMultiBedUrl file.bb</code></div> </TD></TR> <TR VALIGN=TOP><TD class="hideEmptySubtracksSourcesUrl"><A name="hideEmptySubtracksSourcesUrl"></A> <IMG class='toggle detail'> <div class="format"> <code>hideEmptySubtracksSourcesUrl file.tab</code></div> </TD></TR> <TR VALIGN=TOP><TD class="hideEmptySubtracksLabel"><A name="hideEmptySubtracksLabel"></A> <IMG class='toggle detail'> <div class="format"> <code>hideEmptySubtracksLabel <label></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="compositeTrack_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a Composite track:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="subGroups"></A> <TABLE class="settingsTable" id="Composite_-_Subgroups_Settings"> <THEAD><TR><TD><DIV ID="subGroups_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Composite track subgroup settings</TH></TR> <TR VALIGN=TOP><TD class="subGroupN"> <A name="subGroupN"></A><IMG class='toggle detail'> <div class="format"> <code>subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]</code><BR> <code>subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="subGroups"><IMG class='toggle detail'> <div class="format"> <code>subGroups <gTag1=mTag1?> [gTag2= mTag2?]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="dimensions"><A name="dimensions"></A><IMG class='toggle detail'> <div class="format"><code>dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="filterComposite"> <A name="filterComposite"></A><IMG class='toggle detail'> <div class="format"><code>filterComposite <dim[A/B/C][=one]> [dimB dimC ...]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="dimensionAchecked"> <A name="dimensionAchecked"></A><IMG class='toggle detail'> <div class="format"><code>dimension<?>checked <mTag1a> [mTag1b …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="controlledVocabulary"> <A name="controlledVocabulary"></A><IMG class='toggle detail'> <div class="format"><code>controlledVocabulary <pathToFile> <gTag#=mdbVar> [gTag#=mdbVar …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="sortOrder"><A name="sortOrder"></A><IMG class='toggle detail'> <div class="format"><code>sortOrder <gTag#=+/-> [gTag#=- …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="fileSortOrder"><A name="fileSortOrder"></A><IMG class='toggle detail'> <div class="format"><code>fileSortOrder <var=val> [var=val ...]</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="subGroups_example"> <IMG class='toggle detail'> <div class="format"><B>Examples of Composite tracks with Subgroups</B></div> </TD></TR> </TABLE> <BR><BR> <A name="view"></A> <TABLE class="settingsTable" id="Composite_-_Views_Settings"> <THEAD><TR><TD><DIV ID="view_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Composite track View settings </TH></TR> <TR VALIGN=TOP><TD class="view"><IMG class='toggle detail'> <div class="format"> <code>subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]</code><BR> <code>track <viewName></code><BR> <code>view <viewTag></code></div> </TD></TR> <TR VALIGN=TOP><TD class="parent_view"><A name="parent_view"></A><IMG class='toggle detail'> <div class="format"> <code>subGroups view=<vTag1>…</code><BR> <code>parent <viewName> [off/on]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="viewUi"><A name="viewUi"></A><IMG class='toggle detail'> <div class="format"><code>viewUi on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="configurable"><A name="configurable"></A><IMG class='toggle detail'> <div class="format"><code>configurable <off/on></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="view_example"><IMG class='toggle detail'> <div class="format"><B>Example of a Composite track with Views:</B></div> </TD></TR> </TABLE> <BR><BR> <A name="container"><A name="aggregate"><A name="multiWig"></A> <TABLE class="settingsTable" id="Aggregate_or_Overlay_Track_Settings"> <THEAD><TR><TD><DIV ID="container_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Aggregate or Overlay track settings </TH></TR> <TR VALIGN=TOP><TD class="container"><IMG class='toggle detail'> <div class="format"><code>container multiWig</code></div> </TD></TR> <TR VALIGN=TOP><TD class="parent_container"> <A name="parent_container"></A><IMG class='toggle detail'> <div class="format"><code>parent <containerTrack></code></div> </TD></TR> <TR VALIGN=TOP><TD class="aggregate"><IMG class='toggle detail'> <div class="format"><code>aggregate <transparentOverlay/stacked/solidOverlay/none></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showSubtrackColorOnUi"> <A name="showSubtrackColorOnUi"></A><IMG class='toggle detail'> <div class="format"><code>showSubtrackColorOnUi on</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="container_example"> <IMG class='toggle detail'> <div class="format"><B>Example of an Aggregate track:</B></div> </TD></TR> </TABLE> </div></div> <!-- Next section --> <div class="contentBorder"> <A name="customTracks"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Special settings for custom tracks</div> </div> <div class="borderGuard"> <TABLE class="settingsTable" id="Custom_Tracks_Special_Settings"> <THEAD><TR><TD><DIV ID="customTracks_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Custom track specific settings </TH></TR> <TR VALIGN=TOP><TD class="genome"><A name="genome"></A><IMG class='toggle detail'> <div class="format"><code>genome</code></div> </TD></TR> <TR VALIGN=TOP><TD class="offset"><A name="offset"></A><IMG class='toggle detail'> <div class="format"><code>offset</code></div> </TD></TR> <TR VALIGN=TOP><TD> <P>The following trackDb style settings are only set internally by the hgCustom CGI code. </P> </TD></TR> <TR VALIGN=TOP><TD class="browserLines"> <A name="browserLines"></A><IMG class='toggle detail'> <div class="format"><code>browserLines</code></div> </TD></TR> <TR VALIGN=TOP><TD class="dataUrl"><A name="dataUrl"></A><IMG class='toggle detail'> <div class="format"><code>dataUrl</code></div> </TD></TR> <TR VALIGN=TOP><TD class="dbTrackType"><A name="dbTrackType"></A><IMG class='toggle detail'> <div class="format"><code>dbTrackType</code></div> </TD></TR> <TR VALIGN=TOP><TD class="fieldCount"><A name="fieldCount"></A><IMG class='toggle detail'> <div class="format"><code>fieldCount</code></div> </TD></TR> <TR VALIGN=TOP><TD class="firstItemPos"><A name="firstItemPos"></A><IMG class='toggle detail'> <div class="format"><code>firstItemPos</code></div> </TD></TR> <TR VALIGN=TOP><TD class="htmlFile"><A name="htmlFile"></A><IMG class='toggle detail'> <div class="format"><code>htmlFile</code></div> </TD></TR> <TR VALIGN=TOP><TD class="htmlUrl"><A name="htmlUrl"></A><IMG class='toggle detail'> <div class="format"><code>htmlUrl</code></div> </TD></TR> <TR VALIGN=TOP><TD class="initialPos"><A name="initialPos"></A><IMG class='toggle detail'> <div class="format"><code>initialPos</code></div> </TD></TR> <TR VALIGN=TOP> <TD class="inputType"><A name="inputType"></A><IMG class='toggle detail'> <div class="format"><code>inputType</code></div> </TD> </TR> <TR VALIGN=TOP><TD class="itemCount"><A name="itemCount"></A><IMG class='toggle detail'> <div class="format"><code>itemCount</code></div> </TD></TR> <TR VALIGN=TOP><TD class="mafFile"><A name="mafFile"></A><IMG class='toggle detail'> <div class="format"><code>mafFile</code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxChromName"><A name="maxChromName"></A><IMG class='toggle detail'> <div class="format"><code>maxChromName</code></div> </TD></TR> <TR VALIGN=TOP><TD class="origTrackLine"><A name="origTrackLine"></A><IMG class='toggle detail'> <div class="format"><code>origTrackLine</code></div> </TD></TR> <TR VALIGN=TOP><TD class="tdbType"><A name="tdbType"></A><IMG class='toggle detail'> <div class="format"><code>tdbType</code></div> </TD></TR> <TR VALIGN=TOP><TD class="wibFile"><A name="wibFile"></A><IMG class='toggle detail'> <div class="format"><code>wibFile</code></div> </TD></TR> <TR VALIGN=TOP><TD class="wigFile"><A name="wigFile"></A><IMG class='toggle detail'> <div class="format"><code>wigFile</code></div> </TD></TR> </TABLE> </div></div> <!-- Next section --> <div class="contentBorder rejectSection"> <A name="loosers"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Obscure or special case settings. (aka Rejections)</div> </div> <div class="borderGuard"> <H3>Rejected "types":</H3> <P>axt – rare bed 3 variant (replaced with netAlign?), panTro1.axtNetHg16</P> <P> drosophila/dp1/trackDb.ra:type axt dm1</P> <P> human/hg13/trackDb.ra:type axt mm3</P> <P> human/hg15/trackDb.ra:type axt mm3</P> <P> worm/ce1/trackDb.ra:type axt cb1</P> <P> worm/ce2/trackDb.ra:type axt cb1</P> <P>bedLogR – encode 1% test only??? Not found with tdbQuery from *</P> <P> human/encodeTest/wgEncodeMetaCheckTest.ra</P> <P>chromGraph - ??? Not found in tdbQuery -strict from *</P> <P>gff <A HREF="../../../FAQ/FAQformat.html#format3"> http://genome.ucsc.edu/FAQ/FAQformat.html#format3</A></P> <P> Not found in tdbQuery -strict from *</P> <P>gtf <A HREF="../../../FAQ/FAQformat.html#format4"> http://genome.ucsc.edu/FAQ/FAQformat.html#format4</A></P> <P> Not found in tdbQuery -strict from *</P> <P>maf – replaced by wigMaf hg17, tdbQuery -strict: 1 track: fr1.tbaFishBirdCFTR </P> <P> <A HREF="../../../FAQ/FAQformat.html#format5"> http://genome.ucsc.edu/FAQ/FAQformat.html#format5</A></P> <P>net but not netAlign - custom only??? Not found with tdbQuery non strict</P> <P>sample – RARE bed variant, hg15.affyTranscriptome, Affymetrix Transcriptome</P> <P> hg15.hg15Mm3L</P> <P> Completely replaced by type wig and more recently bigWig</P> <A name="miscLosers"></A> <H3>List of Miscellaneous Specal Case, Deprecated, Rejected or Rarely Used Settings</H3> <TABLE class="settingsTable" id="Miscellaneous_Rejected_Settings"> <TR VALIGN=TOP><TH WIDTH=100>Rejected settings</TH><TH WIDTH=100>For Types</TH><TH>Reason</TH> </TR> <TR VALIGN=TOP> <TD class="accession"><A name="accession"></A><code>accession</code></TD> <TD>all <I>ENCODE only</I></TD> <TD>ENCODE only; DEPRCATED (replaced with mdb )</TD> </TR> <TR VALIGN=TOP> <TD class="canPack"><A name="canPack"></A><code>canPack <off/on></code></div></TD> <TD>all</TD> <TD><I>NOT FOR HUBS. Deprecated.</I> <P>Almost tracks can be displayed in the five standard visibilities. However on some track types such as wiggles, <code>squish</code> and <code>pack</code> offer no real advantage over <code>dense</code> and <code>full</code>. By default, these tracks will not offer the less valuable visibilities. Nevertheless, you can make your track offer these visibility choices by turning canPack on. Note: subtracks of composites will always offer all five choices.</P> <P><B>Example:</B></P> <pre> canPack on</pre> </TD></TR> <TR VALIGN=TOP> <TD class="cdsDrawDefault"><A name="cdsDrawDefault"></A> <code>cdsDrawDefault</code></TD><TD>genePred</TD> <TD>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. </TD> </TR> <TR VALIGN=TOP> <TD class="cdsDrawOptions"><A name="cdsDrawOptions"></A> <code>cdsDrawOptions</code></TD><TD>psl</TD> <TD>I have found no documentation and no code that references this setting. Also, I do not see it in our trackDbs. </TD> </TR> <TR VALIGN=TOP> <TD class="cdsEvidence"><A name="cdsEvidence"></A><code>cdsEvidence</code></TD> <TD>genePred</TD> <TD>Used by JK experimental tracks only as either <code>jkgTxCdsEvidence</code> or <code>jkgTxCdsEvidence2</code>. This will show an evidence table named in the setting. </TD> </TR> <TR VALIGN=TOP> <TD class="cell"><A name="cell"></A><code>cell</code></TD> <TD>bed, bedGraph <I>ENCODE only</I></TD> <TD>Obsolete: replaced with metaDb.</TD> </TR> <TR VALIGN=TOP> <TD class="chip"><A name="chip"></A><code>chip</code></TD> <TD>expRatio, bed <I>ENCODE only</I></TD> <TD>DROP (no takers in any of our trackDb.ra files)</TD> </TR> <TR VALIGN=TOP> <TD class="dateSubmitted"><A name="dateSubmitted"></A> <code>dateSubmitted</code></TD> <TD>bedGraph, bed <I>ENCODE only</I></TD> <TD>Obsolete: replaced with metaDb.</TD> </TR> <TR VALIGN=TOP> <TD class="dateUnrestricted"><A name="dateUnrestricted"></A> <code>dateUnrestricted</code></TD> <TD>bed <I>ENCODE only</I></TD> <TD>Obsolete: replaced with metaDb.</TD> </TR> <TR VALIGN=TOP> <TD class="db"><A name="db"></A><code>db</code></TD> <TD>chain, netAlign, genePred, bed 3</TD> <TD>Not found in any of our trackDb.ras. Further, this is the same as assembly so implicit. </TD> </TR> <TR VALIGN=TOP> <TD class="dbProfile"><A name="dbProfile"></A><code>dbProfile</code></TD><TD>all</TD> <TD>In hg18 experimental and cancerGenomics only.</TD> </TR> <TR VALIGN=TOP> <TD class="dividers"><A name="dividers"></A><code>dividers</code></TD> <TD>all</TD> <TD><!-- <I>(Jim says KEEP_UGLY)</I> --> OBSOLETE: use <A onclick="return jumpTo(this);" HREF="#">sortOrder</A> instead.</TD> </TR> <TR VALIGN=TOP> <TD class="endFudge"><A name="endFudge"></A><code>endFudge</code></TD><TD>bed</TD> <TD>Special case for hg17 HGSV Discordant (variation) tracks. Used in hgc to fudge chromEnd, I think. </TD> </TR> <TR VALIGN=TOP> <TD class="ensArchive"><A name="ensArchive"></A><code>ensArchive</code></TD><TD>genePred</TD> <TD>Only in danRer4 Ensembl NonCoding to generate an Ensembl URL.</TD> </TR> <TR VALIGN=TOP> <TD class="ensemblTranscriptIdUrl"><A name="ensemblTranscriptIdUrl"></A> <code>ensemblTranscriptIdUrl</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="ensemblGeneIdUrl"><A name="ensemblGeneIdUrl"></A> <code>ensemblGeneIdUrl</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="ensemblIdUrl"><A name="ensemblIdUrl"></A><code>ensemblIdUrl</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="expProbeTable"><A name="expProbeTable"></A><code>expProbeTable</code></TD> <TD>expRatio</TD> <TD>Can't find code that supports this.Rare: only in human. affyHumanExon "Affy All Exon" </TD> </TR> <TR VALIGN=TOP> <TD class="extTable"><A name="extTable"></A><code>extTable</code></TD><TD>all</TD> <TD>This setting points to a one record table that holds the external filename. This should be replaced by: <A onclick="return jumpTo(this);" HREF="#">track</A>, <A onclick="return jumpTo(this);" HREF="#">table</A> or <A onclick="return jumpTo(this);" HREF="#">bigDataUrl</A>. <P>(rare bigWig hg18.brTestPlus experimental track)</P> </TD> </TR> <TR VALIGN=TOP> <TD class="extraFields"><A name="extraFields"></A><code>extraFields</code></TD><TD>bed</TD> <TD>OBSOLETE: <!-- (Jim hates it) --> replaced by looking up "as" table description. However, that method does not allow for: <UL> <LI> selective inclusion/exclusion of fields</LI> <LI> reordering fields</LI> <LI> formatting titles</LI> </UL> </TD> </TR> <TR VALIGN=TOP> <TD class="filePos"><A name="filePos"></A><code>filePos</code></TD><TD>all</TD> <TD>Can't find this in any of our trackDb.ra files.</TD> </TR> <TR VALIGN=TOP> <TD class="filterTopScorers"><A name="filterTopScorers"></A> <code>filterTopScorers</code></TD> <TD>bed5FloatScoreWithFdr, bed5FloatScore <I>ENCODE only</I></TD> <TD>Currently only used by pilot encode 1%. <P>Presents user option to limit to the top scoring N items. Might be useful in other MariaDB table based tracks but how valuable is it?</P> </TD> </TR> <TR VALIGN=TOP> <TD> <A name="gainColor"></A> <A name="lossColor"></A> <code>gainColor</code><BR> <code>lossColor</code></TD> <TD>bed <I>ENCODE only</I></TD> <TD>Currently only used by pilot encode 1% in hg17.encodeDless. <P>Provides special color for "gain" and "loss" items.</P> </TD> </TR> <TR VALIGN=TOP> <TD class="graphType"><A name="graphType"></A><code>graphType</code></TD> <TD>bedGraph</TD> <TD><!-- <I>(Jim says KEEP)</I> --> Not found in code. Probably typo of graphTypeDefault. (rare hg18.encodeRegulomeDnaseArray) </TD> </TR> <TR VALIGN=TOP> <TD class="hgGene"><A name="hgGene"></A><code>hgGene</code></TD><TD>genePred</TD> <TD>Cannot find code for this. No effect. ???</TD> </TR> <TR VALIGN=TOP> <TD class="informant"><A name="informant"></A><code>informant</code></TD><TD>genePred</TD> <TD>Special setting for N-SCAN genes. Swapped into html description page.</TD> </TR> <TR VALIGN=TOP> <TD class="inputTracksSubgroupDisplay"><A name="inputTracksSubgroupDisplay"></A> <code>inputTracksSubgroupDisplay</code></TD> <TD>bed, factorSource <I>ENCODE only</I></TD> <TD>Only in hg18/hg19 wgEncodeReg*Clustered tracks. In code #ifdef TO_BE_REMOVED.</TD> </TR> <TR VALIGN=TOP> <TD class="itemAttrTbl"><A name="itemAttrTbl"></A><code>itemAttrTbl</code></TD><TD>genePred</TD> <TD>Only used in borEut13. transMapRefGene.</TD> </TR> <TR VALIGN=TOP> <TD class="linesAt"><A name="linesAt"></A><code>linesAt</code></TD><TD>chromGraph</TD> <TD>Unused track type (tdbQuery -strict).</TD> </TR> <TR VALIGN=TOP> <TD class="longlabel"><A name="longlabel"></A><code>longlabel</code></TD><TD>genePred</TD> <TD>Typo, should be <A onclick="return jumpTo(this);" HREF="#">longLabel</A>.</TD> </TR> <TR VALIGN=TOP> <TD class="longLabelClip"><A name="longLabelClip"></A><code>longLabelClip</code></TD> <TD>all</TD> <TD>Only used in sacCer3 (tdbQuery -strict).</TD> </TR> <TR VALIGN=TOP> <TD class="mafDot"><A name="mafDot"></A><code>mafDot</code></TD><TD>wigMaf</TD> <TD>Can't find this in any of our trackDb.ra files and only supported as cart var.</TD> </TR> <TR VALIGN=TOP> <TD class="mafDotDefault"><A name="mafDotDefault"></A><code>mafDotDefault</code></TD> <TD>wigMaf</TD> <TD>Can't find this in any of our trackDb.ra files.</TD> </TR> <TR VALIGN=TOP> <TD class="mapDispatcher"><A name="mapDispatcher"></A><code>mapDispatcher</code></TD> <TD>expRatio</TD> <TD>Only hg17 group "x" [tingwang 2007] and not in C.</TD> </TR> <TR VALIGN=TOP> <TD class="maxScore"><A name="maxScore"></A><code>maxScore</code></TD><TD>broadPeak</TD> <TD>Obsolete, replaced with <A onclick="return jumpTo(this);" HREF="#">scoreFilterLimits</A>. </TD> </TR> <TR VALIGN=TOP> <TD class="metadata"><A name="metadata"></A><code>metadata</code></TD> <TD>all <I>ENCODE only</I></TD> <TD>OBSOLETE: replaced by metaDb. <I>Currently only way for datHubs to have metadata dropdowns. Used by WashU hubs.</I> </TD> </TR> <TR VALIGN=TOP> <TD class="mgiUrl"><A name="mgiUrl"></A><code>mgiUrl</code></TD><TD>bed</TD> <TD>Special case variant of url used by no current tracks (tdbQuery -strict).</TD> </TR> <TR VALIGN=TOP> <TD class="mgiUrlLabel"><A name="mgiUrlLabel"></A><code>mgiUrlLabel</code></TD><TD>bed</TD> <TD>Special case variant of url used by no current tracks (tdbQuery -strict).</TD> </TR> <TR VALIGN=TOP> <TD class="minMax"><A name="minMax"></A><code>minMax</code></TD><TD>chromGraph</TD> <TD>Unused track type (tdbQuery -strict).</TD> </TR> <TR VALIGN=TOP> <TD class="minScore"><A name="minScore"></A><code>minScore</code></TD> <TD>bed, narrowPeak, broadPeak</TD> <TD>Obsolete, replaced with <A onclick="return jumpTo(this);" HREF="#">scoreFilterLimits</A>. </TD> </TR> <TR VALIGN=TOP> <TD class="msaTable"><A name="msaTable"></A><code>msaTable</code></TD> <TD>wig, wigMafProt, wigMaf</TD> <TD>Only hiv tracks use this. Code in wigMaf display and is used to look up species order. </TD> </TR> <TR VALIGN=TOP> <TD class="ncbiAccXref"><A name="ncbiAccXref"></A><code>ncbiAccXref</code></TD><TD>bed</TD> <TD>Special case used by hg17/hg18 kiddEichler tracks. Names a table to convert kiddEichler IDs to NCBI IDs and print links. </TD> </TR> <TR VALIGN=TOP> <TD class="nextItemButton"><A name="nextItemButton"></A><code>nextItemButton</code></TD> <TD>all</TD> <TD><!-- <I>(Jim says LOSE)</I> --> 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. </TD> </TR> <TR VALIGN=TOP> <TD class="noInherit"><A name="noInherit"></A><code>noInherit</code></TD><TD>all</TD> <TD>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:</P> <OL> <LI>in hdb to makesuperChildren inherit settings from their supertrack. This is done by putting the super settings into the child's settings hash.</LI> <LI>tdbQuery where it appears to have no affect.</LI> </OL> </TD> </TR> <TR VALIGN=TOP> <TD class="nonBedFieldsLabel"><A name="nonBedFieldsLabel"></A> <code>nonBedFieldsLabel</code></TD> <TD>bigBed</TD> <TD>OBSOLETE when bigBed has "as" definitions. Instead, the extraFieldsPrint should pick up the non-standard bed fields straight from the as definition. </TD> </TR> <TR VALIGN=TOP> <TD class="notNCBI"><A name="notNCBI"></A><code>notNCBI</code></TD><TD>bed</TD> <TD>Only used in drosophila dm2/dm3. Referenced in hgc.c code.</TD> </TR> <TR VALIGN=TOP> <TD class="ococci"><A name="ococci"></A><code>ococci</code></TD><TD>bed</TD> <TD>Not referenced in any of our trackDb.ra files or in code.</TD> </TR> <TR VALIGN=TOP> <TD class="otherOrg"><A name="otherOrg"></A><code>otherOrg</code></TD><TD>chain, netAlign</TD> <TD>Typo: should be <A onclick="return jumpTo(this);" HREF="#">otherDb</A>.</TD> </TR> <TR VALIGN=TOP> <TD class="onlyVisibility"><A name="onlyVisibility"></A><code>onlyVisibility</code></TD> <TD>all</TD> <TD>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 "<code>full</code>". (rare hg19.lincRNAsAllCellTypeTopView) </TD> </TR> <TR VALIGN=TOP> <TD class="otherDbTable"><A name="otherDbTable"></A><code>otherDbTable</code></TD><TD>bed</TD> <TD>Special case for Jackson lab's QTL (Quantitative Trait Locus) tracks.</TD> </TR> <TR VALIGN=TOP> <TD class="pairedEndUrlFormat"><A name="pairedEndUrlFormat"></A> <code>pairedEndUrlFormat</code></TD><TD>bed</TD> <TD>Special case only used on kiddEichler track. This is another external URL variant.</TD> </TR> <TR VALIGN=TOP> <TD class="pairwise"><A name="pairwise"></A><code>pairwise</code></TD><TD>wigMaf</TD> <TD>Deprecate, replaced by <A onclick="return jumpTo(this);" HREF="#">summary</A>.</TD> </TR> <TR VALIGN=TOP> <TD class="patDb"><A name="patDb"></A><code>patDb</code></TD><TD>expRatio</TD> <TD>Only hg17 group "x" [jzhu 2007] and not referenced in C.</TD> </TR> <TR VALIGN=TOP> <TD class="patKey"><A name="patKey"></A><code>patKey</code></TD><TD>expRatio</TD> <TD>Only hg17 group "x" [jzhu 2007] and not referenced in C.</TD> </TR> <TR VALIGN=TOP> <TD class="patTable"><A name="patTable"></A><code>patTable</code></TD><TD>expRatio</TD> <TD>Only hg17 group "x" [jzhu 2007] and not referenced in C.</TD> </TR> <TR VALIGN=TOP> <TD class="pgDbLink"><A name="pgDbLink"></A><code>pgDbLink</code></TD><TD>bed</TD> <TD><I>Special only used in hg18/hg19 Genome Variants so far.</I></P> <P>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.</P> <P><B>Example:</B></P> <pre> pgDbLink pgKb1PhenCode pgKb1Snpedia pgKb1Hgmd</pre> </TD> </TR> <TR VALIGN=TOP> <TD class="private"><A name="private"></A><code>private</code></TD><TD>bed</TD> <TD>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. </TD> </TR> <TR VALIGN=TOP> <TD class="pslTable"><A name="pslTable"></A><code>pslTable</code></TD><TD>bed</TD> <TD>Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same <code>illuminaProbesAlign</code> when track is "illuminaProbesAlign".) Used for making an hgcAnchor <code>htcIlluminaProbesAlign</code>. </TD> </TR> <TR VALIGN=TOP> <TD class="pubsArticleTable"><A name="pubsArticleTable"></A><code>pubsArticleTable</code></TD> <TD>bed, psl</TD> <TD>Special for publications track.</TD> </TR> <TR VALIGN=TOP> <TD class="pubsMarkerTable"><A name="pubsMarkerTable"></A> <code>pubsMarkerTable</code></TD><TD>bed, psl</TD> <TD>Special for publications track.</TD> </TR> <TR VALIGN=TOP> <TD class="pubsPslTrack"><A name="pubsPslTrack"></A><code>pubsPslTrack</code></TD> <TD>bed, psl</TD> <TD>Special for publications track.</TD> </TR> <TR VALIGN=TOP> <TD class="pubsSequenceTable"><A name="pubsSequenceTable"></A> <code>pubsSequenceTable</code></TD><TD>bed, psl</TD> <TD>Special for publications track.</TD> </TR> <TR VALIGN=TOP> <TD class="refSeqAnnoVersion"><A name="refSeqAnnoVersion"></A> <code>refSeqAnnoVersion</code></TD><TD>genePred</TD> <TD>Special for rheMac2.refSeqAnno track. Not found in code.</TD> </TR> <TR VALIGN=TOP> <TD class="scoreFilterMax"><A name="scoreFilterMax"></A><code>scoreFilterMax</code></TD> <TD>bed, bedLogR, peptideMapping, bigBed</TD> <TD>OBSOLETE: replaced by <A onclick="return jumpTo(this);" HREF="#">scoreFilterLimits</A> </TD> </TR> <TR VALIGN=TOP> <TD class="searchMethod"><A name="searchMethod"></A><code>searchMethod</code></TD> <TD>bed</TD> <TD>Error. Should be part of searchTable stanza, not track stanza. <P><I>TODO: Document searchTable stanza.</I></P> </TD> </TR> <TR VALIGN=TOP> <TD class="searchType"><A name="searchType"></A><code>searchType</code></TD><TD>bed</TD> <TD>Error. Should be part of searchTable stanza, not track stanza. <P><I>TODO: Document searchTable stanza.</I></P> </TD> </TR> <TR VALIGN=TOP> <TD class="selectSubject"><A name="selectSubject"></A><code>selectSubject</code></TD> <TD>psl</TD> <TD>Special only used in hiv(only used by hiv and h1n1. (Just h1n1 according to tdbQuery -strict). </TD> </TR> <TR VALIGN=TOP> <TD class="seqTable"><A name="seqTable"></A><code>seqTable</code></TD><TD>bed</TD> <TD>Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same <code>illuminaProbesSeq</code> when track is "illuminaProbesAlign".) Used for making an hgcAnchor <code>htcIlluminaProbesAlign</code>. </TD> </TR> <TR VALIGN=TOP> <TD class="settingsByView"><A name="settingsByView"></A><code>settingsByView</code></TD> <TD>all</TD> <TD>OBSOLETE: replaced with "view in the middle" <A onclick="return jumpTo(this);" HREF="#">view</A> as separate track. </TD> </TR> <TR VALIGN=TOP> <TD class="snpTable"><A name="snpTable"></A><code>snpTable <table></code></TD> <TD>bed <I>gwasCatalog only</I></TD> <TD>Special for gwasCatalog: table used to map dbSNP IDs to genomic coords</TD> </TR> <TR VALIGN=TOP> <TD class="snpVersion"><A name="snpVersion"></A><code>snpVersion</code></TD> <TD>bed <I>gwasCatalog only</I></TD> <TD>Special for gwasCatalog: dbSNP build number of table used to map dbSNP IDs to genomic coords</TD> </TR> <TR VALIGN=TOP> <TD class="speciesTarget"><A name="speciesTarget"></A><code>speciesTarget</code></TD> <TD>wigMaf</TD> <TD>OBSOLETE. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with <BR><code>#define BRANEY_SAYS_USETARG_IS_OBSOLETE.</code> </TD> </TR> <TR VALIGN=TOP> <TD class="speciesTree"><A name="speciesTree"></A><code>speciesTree</code></TD><TD>wigMaf</TD> <TD>OBSOLETE. Replaced by <A onclick="return jumpTo(this);" HREF="#">treeImage</A>. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with <BR><code>#define BRANEY_SAYS_USETARG_IS_OBSOLETE.</code> </TD> </TR> <TR VALIGN=TOP> <TD class="speciesUseFile"><A name="speciesUseFile"></A> <code>speciesUseFile <fileName></code></TD> <TD>wigMaf</TD> <TD> <P><I>Deprecated</I></P> <P>Much more rarely used, this setting can replace <code>speciesOrder</code> and <code>speciesGroups</code>. Set the <code>speciesUseFile</code> to a path relative to the apache cgi-bin. The file should contain a single species name as the first word of each line.</P> <P><B>Example:</B></P> <pre> speciesUseFile speciesLists/conserved8Way.txt</pre> </TD> </TR> <TR VALIGN=TOP> <TD class="stripPrefix"><A name="stripPrefix"></A><code>stripPrefix</code></TD><TD>bam</TD> <TD><I>Not yet implemented? Only on hg18.oneKGHighCovSeq experimental track.</I></TD> </TR> <TR VALIGN=TOP> <TD class="subgroups"><A name="subgroups"></A><code>subgroups</code></TD><TD>bed</TD> <TD>Typo: should be <A onclick="return jumpTo(this);" HREF="#">subGroups</R>.</TD> </TR> <TR VALIGN=TOP> <TD class="subTrack"><A name="subTrack"></A><code>subTrack</code></TD><TD>all</TD> <TD>OBSOLETE: replaced with <A HREF="#parent">parent</A>.</TD> </TR> <TR VALIGN=TOP> <TD class="symbolTable"><A name="symbolTable"></A><code>symbolTable</code></TD> <TD>bed, genePred</TD> <TD>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). </TD> </TR> <TR VALIGN=TOP> <TD class="txInfo"><A name="txInfo"></A><code>txInfo</code></TD><TD>genePred</TD> <TD>Only seems to be used in <!-- Jim's --> experimental tracks in hg18 and mm8.</TD> </TR> <TR VALIGN=TOP> <TD class="urlName"><A name="urlName"></A><code>urlName</code></TD><TD>genePred</TD> <TD>Not referenced in code and rarely used. (e.g. hg18: encodePseudogeneConsensus, encodePseudogeneYale). </TD> </TR> <TR VALIGN=TOP> <TD class="url2"><A name="url2"></A><code>url2</code></TD><TD>bed</TD> <TD>Special cased second URL used much like <A HREF="#url">url</A>. </TD> </TR> <TR VALIGN=TOP> <TD class="url2Label"><A name="url2Label"></A><code>url2Label</code></TD><TD>bed</TD> <TD>Special cased second URL label used much like <A HREF="#urlLabel">urlLabel</A>. </TD> </TR> <TR VALIGN=TOP> <TD class="useScore"><A name="useScore"></A> <code>useScore</code></TD><TD>bed, factorSource, bed5FloatScore, broadPeak</TD> <TD>Deprecate: replaced with <A onclick="return jumpTo(this);" HREF="#">spectrum</A> as a slighly less obscurely named setting. </TD> </TR> <TR VALIGN=TOP> <TD class="vegaGeneIdUrl"><A name="vegaGeneIdUrl"></A><code>vegaGeneIdUrl</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="vegaTranscriptIdUrl"><A name="vegaTranscriptIdUrl"></A> <code>vegaTranscriptIdUrl</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="visibilityViewDefaults"><A name="visibilityViewDefaults"></A> <code>visibilityViewDefaults</code></TD><TD>all</TD> <TD>OBSOLETE since view in the middle change. LOSE</TD> </TR> <TR VALIGN=TOP> <TD class="wgEncodeGencode"><A name="wgEncodeGencode"></A> <code>wgEncodeGencodeVersion</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeAttrs</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeExonSupport</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeGeneSource</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeTranscriptSource</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodePdb</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodePubMed</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeRefSeq</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeTag</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeTranscriptSupport</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeUniProt</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodePolyAFeature</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeAnnotationRemark</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD><code>wgEncodeGencodeTranscriptionSupportLevel</code></TD> <TD>genePred <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD class="yLinOnOff"><A name="yLinOnOff"></A><code>yLinOnOff</code></TD><TD>wigMaf</TD> <TD> <P>Typo: should be <A onclick="return jumpTo(this);" HREF="#">yLineOnOff</A>.</P> </TD> </TR> <TR VALIGN=TOP> <TD class="yalePseudoAssoc"><A name="yalePseudoAssoc"></A><code>yalePseudoAssoc</code></TD> <TD>all <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode.</TD> </TR> <TR VALIGN=TOP> <TD class="yalePseudoUrl"><A name="yalePseudoUrl"></A><code>yalePseudoUrl</code></TD> <TD>all <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> <TR VALIGN=TOP> <TD class="yaleUrl"><A name="yaleUrl"></A><code>yaleUrl</code></TD> <TD>all <I>ENCODE Gencode Only</I></TD> <TD>Special for ENCODE Gencode to generate external URL.</TD> </TR> </TABLE> </div></div> <!-- Next section --> <div class="contentBorder"> <div class="borderGuard"> <TABLE class="settingsTable" id="toc"></TABLE> </div></div> <!-- - - - - - - - Documentation Library gets filled here with setting DIVs - - - - - - - --> <div id="library"> <!--#include virtual="trackDbLibrary.shtml" --> </div> </BODY></HTML>