483e785a1cef9c2bfe1f08030cbc781f353deffc lrnassar Tue Jun 10 09:01:13 2025 -0700 Doc'ing logoMaf option, refs #34064 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index 28a42387258..eb9fa9670d2 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -1,1570 +1,1574 @@ <!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="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> <!-- Finally to the content --> <div class="borderGuard"> <DIV class="trackDbHub_intro"> <H1>Hub Track Database Definition (<SPAN id="trackDbHub_version">v3</SPAN>)</H1> <H2>How to declare Dataset Display Settings in Genome Browser Hubs</H2> <p>For returning readers: We keep a <a href="changes.html">list of changes</a> to the trackDb specification below.</p> <P>This document describes how to set dataset display characteristics using "track database" or "trackDb" settings through key-value pair associations used in a Track Hub's trackDb.txt file. <P>The text file format for trackDb settings starts by creating a text block, or "stanza", for each track dataset following "ra" rules to establish a "record" of related settings. The first line establishes the <code>track</code> "key", with additional lines containing further "setting" keys, and one or more words or numbers that follow, which are the "values" for each setting. All trackDb stanzas are keyed by <code>track</code> and delimited by blank lines. Here is an example:</P> <pre> track myFirstTrack type bigBed 3 bigDataUrl myFirstTrack.bb shortLabel Example Data longLabel The data in this track is format "bigBed 3". </pre> <P>Every track stanza should have these five settings (<code>track type bigDataUrl shortLabel longLabel</code>). The first line's <code>track</code> key value (<code>myFirstTrack</code>) is the identifier for the dataset given to the Browser and it must be unique for each track within your data hub. After the <code>track</code> key, the most important setting is the <code>type</code> key. This value (<code>bigBed 3</code>) tells the Browser the type of format the data is in, defines how to display it, and determines which options are available for fine control of that display. For some configurable features, like <a href="#filter">filters</a>, an additional period or plus may be needed (<code>bigBed 5 .</code>) or (<code>bigBed 9 +</code>). </P> <P>While there are over 100 settings (providing a high level of flexibility for track display) defined in this document and supported at UCSC, only the above five are <font class="level-required">required</font> to define a track and other sites that display hubs have more limited settings support. To ease the task of hub developers and sites that display hubs, each setting has been assigned a support level. The most commonly used and broadly supported settings have been designated as <font class="level-base">base</font> settings, to foster hub portability. The level for each setting is indicated in this document by color, shown below and in each description section as well as in the <A HREF="#toc">Table of Contents</A>. The support levels are: <table style="margin-left: 50px;"> <tr><td class="level-required">required</td><td>required settings</td></tr> <tr><td class="level-base">base</td><td>common settings supported at other sites</td></tr> <tr><td class="level-deprecated">deprecated</td><td>settings that are being retired (replacement is listed in details section)</td></tr> <tr><td class="level-new">new</td><td>new settings not yet assigned a level (may be replaced)</td></tr> <tr><td class="level-full">full</td><td>other settings</td></tr> </table> </P> <P>This documentation page has also been assigned a version number so that when <font class="level-new">new</font> settings are added, or older settings are <font class="level-deprecated">deprecated</font> other browser sites and track hub builders can verify the hub to the relevant version. To learn about new settings you can view our <a href="http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features" target="_blank">software release log</a> or view news at a collaborative <a href="http://groups.google.com/a/soe.ucsc.edu/group/track-hubs" target="_blank"> track hub mailing list</a>. You can also see the <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/commits/master/src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml" target="_blank">commit history</a> of recent changes to the document library. </P> <p> You can use the <code>hubCheck</code> utility to check the compatibility of your hub and its trackDb settings with the UCSC Genome Browser or other genome browsers, such as Ensembl. Our <a href="../hgTrackHubHelp.html#Compatibility">track hub help page</a> provides some examples of how you might use <code>hubCheck</code> to do this and you can read more in this related <a href="https://genome-blog.gi.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/" target="_blank">blog post.</a></p> </DIV> <h3 id="useOneFile">Use <b><code>useOneFile on</code></b> for hubs with only one genome</h3> <p> This page focuses on the settings found in the <a target="_blank" href="../hgTrackHubHelp.html#trackDb.txt"><code>trackDb.txt</code></a> file; however, all hubs must include a top-level <a target="_blank" href="../hgTrackHubHelp.html#hub.txt"><code>hub.txt</code></a>. If your hub is only displaying one genome, there is a way to put the <a target="_blank" href="../hgTrackHubHelp.html#genomes.txt"><code>genomes.txt</code></a> and <a target="_blank" href="../hgTrackHubHelp.html#trackDb.txt"><code>trackDb.txt</code></a> all into one file. Read about the special <a target="_blank" href="../hgTracksHelp.html#UseOneFile"><code>useOneFile on</code></a> setting to allow all a hub to exist in one file. Load a working example <a target="_blank" href="../examples/hubExamples/hubUseOneFile/singleFileHubExample.txt">here</a>.</p> <h3 id="assembly_hubs">Assembly Hubs</h3> <p> This page focuses on the settings found in the <a target="_blank" href="../hgTrackHubHelp.html#trackDb.txt"><code>trackDb.txt</code></a> file used in both Track Hubs and Assembly Hubs; however, this page does not describe the settings unique to Assembly Hubs. Track Hubs can display novel genomes, through a type of hub called an <a href="../hgTrackHubHelp.html#Assembly" target="_blank">Assembly Hub</a>. The <a href="../hgTrackHubHelp.html#example_genomes.txt" target="_blank"><code>genomes.txt</code></a> file for an Assembly Hub involves many additional settings not described on this page, such as <a href="../hgTrackHubHelp.html#twoBitPath" target="_blank"><code>twoBitPath</code></a> and <a href="../hgTrackHubHelp.html#defaultPos" target="_blank"><code>defaultPos</code></a> to identify the location of the sequence for the novel assembly and what default position to display. The <code>genomes.txt</code> file in Assembly Hubs also requires display information such as <a href="../hgTrackHubHelp.html#organism" target="_blank"><code>organism</code></a>, <a href="../hgTrackHubHelp.html#scientificName" target="_blank"><code>scientificName</code></a>, <a href="../hgTrackHubHelp.html#description" target="_blank"><code>description</code></a>, and <a href="../hgTrackHubHelp.html#htmlPath" target="_blank"><code>htmlPath</code></a> to label the novel assembly on the gateway page. A special <a href="../hgTrackHubHelp.html#groups" target="_blank"><code>groups</code></a> setting in Assembly Hubs points to a separate text document that defines track groups under the main image (such as the first "Mapping and Sequencing" group found on almost all Browsers). Read the <a target="_blank" href="../hgTrackHubHelp.html#genomes.txt">"Create the genomes.txt file"</a> section of the Track Hub User Guide for more information, and see examples in the <a target="_blank" href="../hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs<a>.</p> <P>The remainder of this document is divided into the following sections and should be used as a ready reference.</P> <IMG class='toggle all' /> <I>Expand/close descriptions of settings in the sections below.</I> <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="#bam">bam/cram</A>: Compressed Sequence Alignment/Map tracks</LI> <LI><A HREF="#bigBed_-_Item_or_Region_Track_Settings">bigBed</A>: Item or region tracks</LI> <LI><A HREF="#bigBarChart">bigBarChart</A>: Bar charts of categorical variables displayed over genomic regions</LI> <LI><A HREF="#bigChain_-_Pairwise_Alignments">bigChain</A>: Genome-wide Pairwise Alignments</LI> <LI><A HREF="#bigGenePred_-_Gene_Annotations">bigGenePred</A>: Gene Annotations</LI> <LI><A HREF="#bigInteract">bigInteract</A>: Pairwise interactions</LI> <LI><A HREF="#bigLolly">bigLolly</A>: Lollipops</LI> <LI><A HREF="#bigNarrowPeak_-_Peaks">bigNarrowPeak</A>: Peaks</LI> <LI><A HREF="#bigMaf_-_Multiple_Alignments">bigMaf</A>: Mulitple Alignments</LI> <LI><A HREF="#bigPsl_-_Pairwise_Alignments">bigPsl</A>: Pairwise Alignments</LI> <LI><A HREF="#bigWig_-_Signal_Graphing_Track_Settings">bigWig</A>: Signal graphing tracks</LI> <LI><A HREF="#hic">hic</A>: Hi-C contact matrices</LI> <LI><A HREF="#halSnake">halSnake</A>: HAL Snake Format</LI> <LI><A HREF="#vcfTabix">vcfTabix</A>: Variant Call Format</LI> <LI><A HREF="#vcfPhasedTrio">vcfPhasedTrio</A>: Variant Call Format Trios</LI> </UL></LI> <LI><A HREF="#groupingTracks">Grouping tracks into sets and hierarchies</A> – with examples <UL> <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="#toc">Table of Contents</A></LI> </OL> </div></div> <!-- Settings specification --> <div id="specification"> <!-- 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 class="level-required">track</code></div> </TD></TR> <TR VALIGN=TOP><TD class="type"><A name="type"></A><IMG class='toggle detail'> <div class="format"><code class="level-required">type</code></div> </TD></TR> <TR VALIGN=TOP><TD class="shortLabel"><A name="shortLabel"></A><IMG class='toggle detail'> <div class="format"><code class="level-required">shortLabel</code></div> </TD></TR> <TR VALIGN=TOP><TD class="longLabel"><A name="longLabel"></A><IMG class='toggle detail'> <div class="format"><code class="level-required">longLabel</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><A name="bigDataUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="html"><A name="html"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">html</code></div> </TD></TR> <TR VALIGN=TOP><TD class="visibility"><A name="visibility"></A><IMG class='toggle detail'> <div class="format"><code class="level-required">visibility</code></div> </TD></TR> <TR VALIGN=TOP><TD class="meta"><A name="meta"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">meta</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="color"><A name="color"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">color <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="priority"><A name="priority"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">priority <float></code></div> </TD></TR> <TR VALIGN=TOP><TD class="altColor"><A name="altColor"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">altColor <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="boxedCfg"><A name="boxedCfg"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">boxedCfg <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromosomes"><A name="chromosomes"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">chromosomes <chr1,chr2,...></code></div> </TD></TR> <TR VALIGN=TOP><TD class="darkerLabels"><A name="darkerLabels"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">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 class="level-full">dataVersion <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="directUrl_for_hubs"><A name="directUrl_for_hubs"></A> <A name="directUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">directUrl <url></code></div> </TD></TR> <TR VALIGN=TOP><TD class="downloadUrl"><A name="downloadUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">downloadUrl <label> <URL></code></div> </TD></TR> <TR VALIGN=TOP><TD class="iframeUrl"><A name="iframeUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">iframeUrl <url></code></div> </TD></TR> <TR VALIGN=TOP><TD class="iframeOptions"><A name="iframeOptions"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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>multiRegionsBedUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherDb"><A name="otherDb"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">otherDb <otherDb></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">otherTwoBitUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="pennantIcon"><A name="pennantIcon"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">pennantIcon <iconFile>/<text color> [html [tip]] [; <iconFile>/<text color> [html [tip]]]</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_for_hubs"> <A name="url"></A> <A name="urlLabel"></A><IMG class='toggle detail'> <div class="format"> <span class="url"><code class="level-full">url <url></code></span><BR> <span class="urlLabel"><code class="level-full">urlLabel <label></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="urls"><A name="urls"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">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 class="level-full">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 class="level-full">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 class="level-full">sepFields fieldName1,fieldName2 ...</code><BR> </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. Many of these tracks are described below along with settings specific to their types.</P> <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 class="level-required">bigDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="refUrl"><A name="refUrl"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">refUrl <url></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataIndex"><A name="bigDataIndex"></A> <IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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 class="level-full">bamGrayMode <aliQual/baseQual/unpaired></code><BR> <span class="aliQualRange"><code class="level-full">aliQualRange <min:max></code></span><BR> <span class="baseQualRange"><code class="level-full">baseQualRange <min:max></code><</span></div> </TD></TR> <TR class="related" VALIGN=TOP><TD class="bamColorTag"> <A name="bamColorTag"></A><IMG class='toggle detail setD'> <div class="format"><code class="level-full">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 class="level-full">noColorTag .</code></div> </TD></TR> <TR VALIGN=TOP><TD class="bamSkipPrintQualScore"><A name="bamSkipPrintQualScore"></A> <IMG class='toggle detail'> <div class="format"><code class="level-full">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"> <span class="indelDoubleInsert"><code class="level-full">indelDoubleInsert <off/on></code></span><BR> <span class="indelQueryInsert"><code class="level-full">indelQueryInsert <off/on></code></span><BR> <span class="indelPolyA"><code class="level-full">indelPolyA <off/on></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="minAliQual"><A name="minAliQual"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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 class="level-full">pairSearchRange <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showNames"><A name="showNames"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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="#">maxWindowCoverage</A>, <A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>, </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bam_example"><IMG class='toggle detail'> <div class="format"><B>Example of a 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-full">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> </td></tr> <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> </td></tr> <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-full"> 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="barChartFacets"><a name="barChartFacets"></a> <img class='toggle detail'> <div class="format"><code class="level-new"> barChartFacets on</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 on</code> </div> </td></tr> <tr valign=top><td class="barChartMerge"><a name="barChartMerge"></a> <img class='toggle detail'> <div class="format"><code class="level-new"> barChartMerge 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> </td></tr> <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> </td></tr> <tr valign=top><td class="barChartCategoryUrl"><a name="barChartCategoryUrl"></a> <img class='toggle detail'> <div class="format"><code class="level-full">barChartCategoryUrl <url/relativePath></code> </div> </td></tr> <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> </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"><A name="maxLimit"></A><img class='toggle detail'> <div class="format"><code class="level-full">maxLimit <maximum-bar-value></code> </div> </td></tr> <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="bigBed"></A> <TABLE class="settingsTable" id="bigBed_-_Item_or_Region_Track_Settings"> <THEAD><TR><TD><DIV ID="bigBed_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigBed - Item or region track settings </TH></TR> <TR VALIGN=TOP><TD class="bigBed"><IMG class='toggle detail'> <div class="format"> <code>type bigBed <3-12> [+/.]</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="itemRgb"><A name="itemRgb"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">itemRgb on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="colorByStrand"><A name="colorByStrand"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">colorByStrand <red,green,blue> <red,green,blue></code></div> </TD></TR> <TR VALIGN=TOP><TD class="denseCoverage"><A name="denseCoverage"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">denseCoverage <maxVal></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelOnFeature"><A name="labelOnFeature"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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 class="level-full">exonNumbers <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="scoreFilter"> <A name="scoreFilter"></A> <A name="scoreFilterLimits"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">scoreFilter <low>[:<high>]</code><BR> <span class="scoreFilterLimits"><code class="level-full">scoreFilterLimits <low>[:<high>]</code></span><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="maxItems"><A name="maxItems"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">maxItems <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowCoverage"> <A name="maxWindowCoverage"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">maxWindowCoverage <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowToDraw"> <A name="maxWindowToDraw"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">maxWindowToDraw <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="minGrayLevel"><A name="minGrayLevel"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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 class="level-base">spectrum on</code><BR> <span class="scoreMax"><code class="level-full">scoreMax <integer></code></span><BR> <span class="scoreMin"><code class="level-full">scoreMin <integer></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="thickDrawItem"><A name="thickDrawItem"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-new">decorator.*</code></div> </TD></TR> <TR VALIGN=TOP><TD class="searchIndex"><A name="searchIndex"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">searchIndex <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="searchTrix"><A name="searchTrix"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">searchTrix <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><A name="labelFields"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><A name="defaultLabelFields"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelSeparator"><A name="labelSeparator"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">labelSeparator <text></code></div> </TD></TR> <TR VALIGN=TOP><TD class="filter"><A name="filter"></A> <A name="filter.fieldName"></A> <A name="filterLimits.fieldName"></A> <A name="filterByRange.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filter.<fieldName> <default integer></code><BR> <span class="filterByRange"><code class="level-full">filterByRange.<fieldName> <off/on></code></span><BR> <span class="filterLimits"><code class="level-full">filterLimits.<fieldName> <low>[:<high>]</code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="filterText"><A name="filterText"></A> <A name="filterText.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterText.<fieldName> <default search string></code><BR> <span class="filterType"><code class="level-full">filterType.<fieldName> <wildcard/regexp></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="filterValues"><A name="filterValues"></A> <A name="filterValues.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterValues.<fieldName> <value1,value2,value3...></code><BR> <span class="filterValuesDefault"><code class="level-full">filterValuesDefault.<fieldName> <value1,value2,value3...></code></span><BR> <span class="filterType"><code class="level-full">filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="filterLabel"><A name="filterLabel"></A> <A name="filterLabel.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterLabel.<fieldName> <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="highlight"><A name="highlight"></A> <A name="highlight.fieldName"></A> <A name="highlightLimits.fieldName"></A> <A name="highlightByRange.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-new">highlight.<fieldName> <default integer></code><BR> <span class="highlightByRange"><code class="level-new">highlightByRange.<fieldName> <off/on></code></span><BR> <span class="highlightLimits"><code class="level-new">highlightLimits.<fieldName> <low>[:<high>]</code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="highlightText"><A name="highlightText"></A> <A name="highlightText.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-new">highlightText.<fieldName> <default search string></code><BR> <span class="highlightType"><code class="level-new">highlightType.<fieldName> <wildcard/regexp></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="highlightValues"><A name="highlightValues"></A> <A name="highlightValues.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-new">highlightValues.<fieldName> <value1,value2,value3...></code><BR> <span class="highlightValuesDefault"><code class="level-new">highlightValuesDefault.<fieldName> <value1,value2,value3...></code></span><BR> <span class="highlightType"><code class="level-new">highlightType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="highlightColor"><A name="highlightColor"></A> <A name="highlightColor"</A><IMG class='toggle detail'> <div class="format"> <code class="level-new">highlightColor <#hexcolor></code><BR> </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="bedNameLabel"><A name="bedNameLabel"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">bedNameLabel <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="exonArrowsDense"> <A name="exonArrowsDense"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">exonArrowsDense <off/on></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 class="level-full">itemImagePath <path> <suffix></code><BR> <span class="itemBigImagePath"><code class="level-full">itemBigImagePath <path> <suffix></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="mergeSpannedItems"><A name="mergeSpannedItems"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">mergeSpannedItems <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="linkIdInName"><A name="linkIdInName"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">linkIdInName on</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 class="level-full">nextExonText <str></code><BR> <span class="prevExonText"><code class="level-full">prevExonText <str></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="scoreLabel"><A name="scoreLabel"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">scoreLabel <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showTopScorers"> <A name="showTopScorers"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">showTopScorers #</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bigBed_example"> <A name="bigBed_Examples"></A><IMG class='toggle detail'> <div class="format"><B>Examples of item base types</B></div> </TD></TR> </TABLE> <BR><BR> <A name="bigChain"></A> <TABLE class="settingsTable" id="bigChain_-_Pairwise_Alignments"> <THEAD><TR><TD><DIV ID="bigChain_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigChain - Genome-wide Pairwise Alignments </TH></TR> <TR VALIGN=TOP><TD class="bigChain"><IMG class='toggle detail'> <div class="format"> <code>type bigChain</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="linkDataUrl"><A name="linkDataUrl"</A><IMG class='toggle detail'> <div class="format"><code class="level-full">linkDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"</A><IMG class='toggle detail'> <div class="format"><code class="level-new">otherTwoBitUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorUseSequence"><A name="baseColorUseSequence"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit ></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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"> <span class="indelDoubleInsert"><code class="level-full">indelDoubleInsert <off/on></code></span><BR> <span class="indelQueryInsert"><code class="level-full">indelQueryInsert <off/on></code></span><BR> <span class="indelPolyA"><code class="level-full">indelPolyA <off/on></code></span></div> </TD></TR> </TABLE> <BR><BR> <A name="bigGenePred"></A> <TABLE class="settingsTable" id="bigGenePred_-_Gene_Annotations"> <THEAD><TR><TD><DIV ID="bigGenePred_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigGenePred - Gene Annotations </TH></TR> <TR VALIGN=TOP><TD class="bigGenePred"><IMG class='toggle detail'> <div class="format"> <code>type bigGenePred</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="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full"> baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelSeparator"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelSeparator <text></code></div> </TD></TR> <tr valign=top><td> <p>Additional settings defined in other sections are also available for displaying bigGenePred tracks.</p> <a onclick="return jumpTo(this);" HREF="#">decorator</a> </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 class="endsVisible"><a name="endsVisible"></a> <img class='toggle detail'> <div class="format"> <code class="level-full">endsVisible two</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="bigMaf"></A> <TABLE class="settingsTable" id="bigMaf_-_Multiple_Alignments"> <THEAD><TR><TD><DIV ID="bigMaf_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigMaf - Multiple alignments </TH></TR> <TR VALIGN=TOP><TD class="bigMaf"><IMG class='toggle detail'> <div class="format"> <code>type bigMaf</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="speciesOrder"><A name="speciesOrder"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">speciesOrder <species1> [species2 …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="speciesLabels"><A name="speciesLabels"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">speciesLabels <species1=newLabel1> [species2=newLabel2 …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="frames"><A name="frames"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">frames <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="summary"><A name="summary"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">summary <tableName/url></code></div> </TD></TR> </TABLE> <BR><BR> <A name="bigNarrowPeak"></A> <TABLE class="settingsTable" id="bigNarrowPeak_-_Peaks"> <THEAD><TR><TD><DIV ID="bigNarrowPeak_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigNarrowPeak - Peaks </TH></TR> <TR VALIGN=TOP><TD class="bigNarrowPeak"><IMG class='toggle detail'> <div class="format"> <code>type bigNarrowPeak</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="Filter"> <A name="Filter"></A> <A name="pValueFilter"></A> <A name="qValueFilter"></A> <A name="signalFilter"></A><IMG class='toggle detail'> <div class="format"> <span class="pValueFilter"><code class="level-full">pValueFilter</code></span><BR> <span class="qValueFilter"><code class="level-full">qValueFilter</code></span><BR> <span class="signalFilter"><code class="level-full">signalFilter</code></span></div> </div> </TD></TR> </TABLE> <BR><BR> <A name="bigPsl"></A> <TABLE class="settingsTable" id="bigPsl_-_Pairwise_Alignments"> <THEAD><TR><TD><DIV ID="bigPsl_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigPsl - Pairwise Alignments </TH></TR> <TR VALIGN=TOP><TD class="bigPsl"><IMG class='toggle detail'> <div class="format"> <code>type bigPsl</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="baseColorUseCds"><A name="baseColorUseCds"><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseCds <given></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorUseSequence"><A name="baseColorUseSequence"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss ></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesAllScales"><A name="showDiffBasesAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">showDiffBasesAllScales on</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"> <span class="indelDoubleInsert"><code class="level-full">indelDoubleInsert <off/on></code></span><BR> <span class="indelQueryInsert"><code class="level-full">indelQueryInsert <off/on></code></span><BR> <span class="indelPolyA"><code class="level-full">indelPolyA <off/on></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="pslSequence"><A name="pslSequence"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">pslSequence <no/all/different></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showCdsAllScales"><A name="showCdsAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsAllScales on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="showCdsMaxZoom"><A name="showCdsMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesMaxZoom"><A name="showDiffBasesMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showDiffBasesMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelSeparator"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelSeparator <text></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"</A><IMG class='toggle detail'> <div class="format"><code class="level-new">otherTwoBitUrl <url/relativePath></code></div> </TD></TR> <tr valign=top><td> <p>Additional settings defined in other sections are also available for displaying bigPsl tracks.</p> <a onclick="return jumpTo(this);" HREF="#">decorator</a> </TABLE> <BR><BR> <A name="bigWig"> <TABLE class="settingsTable" id="bigWig_-_Signal_Graphing_Track_Settings"> <THEAD><TR><TD><DIV ID="bigWig_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigWig - Signal graphing track settings </TH></TR> <TR VALIGN=TOP><TD class="bigWig"><IMG class='toggle detail'> <div class="format"> <code>type bigWig <#> <#></code></div> </TD></TR> <TR VALIGN=TOP><TD class="autoScale"><A name="autoScale"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">autoScale <off/on/group></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxHeightPixels"> <A name="maxHeightPixels"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">maxHeightPixels <max:default:min></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 class="level-base">viewLimits <lower:upper></code><BR> <span class="viewLimitsMax"><code class="level-full">viewLimitsMax <lower:upper></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="alwaysZero"><A name="alwaysZero"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">alwaysZero <off/on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">graphTypeDefault points</code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxWindowToQuery"> <A name="maxWindowToQuery"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">maxWindowToQuery <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="negateValues"> <A name="negateValues"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">negateValues <on></code></div> </TD></TR> <TR VALIGN=TOP><TD class="setColorWith"> <A name="setColorWith"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">setColorWith <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="smoothingWindow"> <A name="smoothingWindow"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">transformFunc <NONE/LOG></code></div> </TD></TR> <TR VALIGN=TOP><TD class="logo"> <A name="logo"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">logo on</code></div> </TD></TR> + <TR VALIGN=TOP><TD class="logoMaf"> + <A name="logoMaf"></A><IMG class='toggle detail'> + <div class="format"><code class="level-new">logoMaf <url/relativePath></code></div> + </TD></TR> <TR VALIGN=TOP><TD class="windowingFunction"> <A name="windowingFunction"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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"> <span class="yLineMark"><code class="level-full">yLineMark <#></code></span><BR> <span class="yLineOnOff"><code class="level-full">yLineOnOff <off/on></code></span><BR> <span class="gridDefault"><code class="level-full">gridDefault on</code></span></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="bigWig_example"><IMG class='toggle detail'> <div class="format"><B>Examples of signal graphing tracks</B></div> </TD></TR> </TABLE> <BR><BR> <A name="bigLolly"></A> <TABLE class="settingsTable" id="bigLolly - Lollipop charts"> <THEAD><TR><TD><DIV ID="bigLolly_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigLolly - lollipop graphs </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"><a name="noStems"<a/><img class='toggle detail'> <div class="format"><code class="level-full">noStems <on/off></code> </div> </td></tr> <tr valign=top><td class="lollySizeField"><a name="lollySizeField"<a/><img class='toggle detail'> <div class="format"><code class="level-full">lollySizeField <integer></code> </div> </td></tr> <tr valign=top><td class="lollyMaxSize"><a name="lollyMaxSize"<a/><img class='toggle detail'> <div class="format"><code class="level-full">lollyMaxSize <integer></code> </div> </td></tr> <tr valign=top><td class="lollyField"><a name="lollyField"<a/><img class='toggle detail'> <div class="format"><code class="level-full">lollyField <integer></code> </div> </td></tr> <tr valign=top><td class="yAxisLabel"><a name="yAxisLabel"<a/><img class='toggle detail'> <div class="format"><code class="level-full">yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string> </code></div> </td></tr> <tr valign=top><td class="yAxisNumLabels"><a name="yAxisNumLabels"<a/><img class='toggle detail'> <div class="format"><code class="level-full">yAxisNumLabels <on/off></code> </div> </td></tr> </TABLE> <BR><BR> <A name="hic"></A> <TABLE class="settingsTable" id="hic_-_Hi-C contact matrices"> <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 class="level-required">bigDataUrl <url/relativePath></code></div> </TD></TR> <tr valign=top><td class="color"><img class='toggle detail'> <div class="format"><code class="level-base">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 class="level-full">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 class="level-full">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 class="level-full">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 class="level-full">saturationScore <float></code></div> </td></tr> <tr valign=top><td class="autoScale"><a name="autoScale"></a><img class='toggle detail'> <div class="format"><code class="level-base">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 class="level-new">hicDistanceMin <integer></code></div> </td></tr> <tr valign=top><td class="hicDistanceMax"><a name="hicDistanceMax"></a><img class='toggle detail'> <div class="format"><code class="level-new">hicDistanceMax <integer></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="halSnake"></A> <TABLE class="settingsTable" id="halSnake_-_Multiple_Alignments"> <THEAD><TR><TD><DIV ID="halSnake_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> halSnake - Genome-wide Multiple Alignments </TH></TR> <TR VALIGN=TOP><TD class="halSnake"><IMG class='toggle detail'> <div class="format"> <code>type halSnake</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="showSnpWidth"><A name="showSnpWidth"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">showSnpWidth <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherSpecies"><A name="otherSpecies"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">otherSpecies <otherSpecies></code></div> </TD></TR> </TABLE> <BR><BR> <a name="vcf"></a> <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 class="level-required">bigDataUrl <url/relativePath></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 class="related1st" VALIGN=TOP><TD class="hapClusterEnabled"><A NAME="hapClusterEnabled"><IMG class='toggle detail setF'> <div class="format"><I>Related settings:</I><BR> <code class="level-full">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">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-full">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 class="level-full">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 class="level-full">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 class="level-full">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 class="level-full">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 class="level-full">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-full">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-full">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoMaf"><A NAME="vcfDoMaf"><IMG class='toggle detail'> <div class="format"><code class="level-full">vcfDoMaf <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"><a name="vcfChildSample"</a><IMG class='toggle detail'> <div class="format"><code class="level-full">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-full">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-full">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-full">vcfDoQual <on/off></code></div> </TD></TR> <TR VALIGN=TOP><TD class="vcfDoMaf"><A NAME="vcfDoMaf"><IMG class='toggle detail'> <div class="format"><code class="level-full">vcfDoMaf <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="vcfPhasedTrio_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a VCF Phased Trio 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"> 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> <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) settings </TH></TR> <TR VALIGN=TOP><TD class="superTrack"><IMG class='toggle detail'> <div class="format"><code class="level-base">superTrack on show</code></div> </TD></TR> <TR VALIGN=TOP><TD class="parent_supertrack"> <A name="parent_supertrack"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">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_hub_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="parent"><A name="parent"></A><IMG class='toggle detail'> <div class="format"><code class="level-base">parent <composite> [off/on]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="compositeTrack"><IMG class='toggle detail'> <div class="format"><code class="level-base">compositeTrack on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="allButtonPair"><A name="allButtonPair"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">allButtonPair on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="centerLabelsDense"> <A name="centerLabelsDense"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">dragAndDrop subTracks</code></div> </TD></TR> <TR VALIGN=TOP><TD class="hideEmptySubtracks"><A name="hideEmptySubtracks"></A> <IMG class='toggle detail'> <div class="format"> <code class="level-full">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 class="level-full">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 class="level-full">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 class="level-full">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 class="level-base">subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]</code><BR> <code class="level-base">subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b=mTitle2b…]</code><BR> <code class="level-base">subGroup3</code> <code class="level-base">subGroup4</code> <code class="level-base">subGroup5</code> <code class="level-base">subGroup6</code> <code class="level-base">subGroup7</code> <code class="level-base">subGroup8</code> <code class="level-base">subGroup9</code> </div> </TD></TR> <TR VALIGN=TOP><TD class="subGroups"><IMG class='toggle detail'> <div class="format"> <code class="level-base">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 class="level-base">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 class="level-full">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 class="level-full">dimensionAchecked <mTag1a> [mTag1b …]</code><BR> <code class="level-full">dimensionBchecked</code> <code class="level-full">dimensionCchecked</code> </div> </TD></TR> <TR VALIGN=TOP><TD class="sortOrder"><A name="sortOrder"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">sortOrder <gTag#=+/-> [gTag#=- …]</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="subGroups_hub_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 class='level-base'>subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]</code><BR> <code class='level-required'>track <viewName></code><BR> <span class="view"><code class="level-full">view <viewTag></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="parent_view"><A name="parent_view"></A><IMG class='toggle detail'> <div class="format"> <code class="level-base">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 class="level-full">viewUi on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="configurable"><A name="configurable"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">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 class="level-base">parent <containerTrack></code></div> </TD></TR> <TR VALIGN=TOP><TD class="aggregate"><IMG class='toggle detail'> <div class="format"><code class="level-full">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 class="level-full">showSubtrackColorOnUi on</code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="container_hub_example"> <IMG class='toggle detail'> <div class="format"><B>Example of an Aggregate track</B></div> </TD></TR> </TABLE> </div></div> <!-- Deprecated settings --> <div class="contentBorder"> <div class="borderGuard"> <A name="Deprecated"></A> <H3>Miscellaneous Deprecated Settings</H3> <TABLE class="settingsTable" id="Miscellaneous_Deprecated_Settings"> <TR VALIGN=TOP><TH WIDTH=100>Setting</TH><TH WIDTH=100>For Types</TH><TH>Notes</TH></TR> <TR VALIGN=TOP> <TD class="metadata"><A name="metadata"></A><code class="level-deprecated">metadata</code> </TD> <TD>all</TD><TD></TD> </TR> <TR VALIGN=TOP> <TD class="noInherit"><A name="noInherit"></A><code class="level-deprecated">noInherit</code></TD><TD>all</TD><TD></TD> </TR> <TR VALIGN=TOP> <TD class="useScore"><A name="useScore"></A> <code class="level-deprecated">useScore</code></TD> <TD>bed, factorSource, bed5FloatScore, broadPeak</TD> <TD>Replaced with <A onclick="return jumpTo(this);" HREF="#">spectrum</A>.</TD> </TR> </TABLE> </div> </div> <!-- End of specs --> </div> <!-- Next section --> <div class="contentBorder"> <div class="borderGuard"> <TABLE class="settingsTable" id="toc"></TABLE> </div></div> <!-- Plain text --> <!-- QA (BL) suggested removing this (leaving code in for now) <pre id="plainToc"> </pre> </div> --> <!-- - - - - - - - Documentation Library gets filled here with setting DIVs - - - - - - - --> <div id="library"> <!--#include virtual="trackDbLibrary.shtml" --> </div> </BODY></HTML>