08afd09bf225ea50691998f829926e9d71d55b49 lrnassar Wed Mar 11 19:21:42 2026 -0700 Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index b157887f9c1..c9c10bcc784 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -1,1781 +1,1781 @@ <!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"--> <!-- Search controls at top level for proper sticky behavior --> <div id="searchDiv"> <div class="search-controls"> <span class="search-label">Search this document:</span> <input id='tdbSearch' type='text' placeholder='e.g. dynseq'></input> </div> <div class="search-actions"> <a href="#TOP" class="search-button secondary" id="jumpToTop">^ Top</a> <button class="search-button" id="clearSearch" type="button">Clear</button> </div> </div> <!--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> This page describes all of the settings one might use in creating a <a href="/goldenPath/help/hgTrackHubHelp.html" target="_blank">track or assembly hub</a>. Hubs display your own data in the Genome Browser by hosting your files on a web server and connecting them with a simple text configuration file, giving you more control and permanence than custom tracks. This initial section touches on the files and settings needed in creating a hub before providing a listing of settings separated by track type.</p> <p> For those new to creating hubs: Our <a href="/docs/hubs/hubBasics.html" target="_blank">Hub Basics</a> page provides a simple introduction to creating hubs.</p> <p> For returning readers: We keep a <a href="changes.html">list of changes</a> to the trackDb specification below.</p> <h3 id="hub_txt">Start with a hub.txt</h3> <p> All hubs must include a top-level hub.txt file. This file contains general settings that identify your hub in our internal databases and in the Genome Browser interface. The URL to the hub.txt is used to load your hub. Our <a href="/docs/hubs/hubBasics.html" target="_blank">Hub Basics</a> describes how to create a hub.txt. A full listing of hub.txt settings can be found in the <a HREF="#hubGeneral">General hub configuration settings</a> section below.</p> <p> If your hub contains tracks on a single genome assembly, then you can put all of the hub, genome, and track configuration settings into a single file with <code><a href="hgTracksHelp.html#UseOneFile" target="_blank">useOneFile</a></code>.</p> <h3 id="genomes_txt">Defining your hub's genomes</h3> <p> A genomes.txt is only necessary if you are <b>NOT</b> using the <code>useOneFile</code> setting as described <a href="#useOneFile">below</a>. When using <code>useOneFile</code>, one only needs to include the <code><a href="#genome">genome</a></code> line. This line will reference a UCSC assembly name (e.g. hg38) or a GenBank assembly available through our <a href="https://hgdownload.gi.ucsc.edu/hubs" target="_blank">GenArk archive</a> beginning with GCF or GCA (e.g. GCF_000891275.1). <p> If your hub contains tracks for more than one genome, you will need to define a <a target="_blank" href="../hgTrackHubHelp.html#genomes.txt"><code>genomes.txt</code></a>. A full listing of genomes.txt settings, including those needed for an <a href="#assembly_hubs">assembly hub</a>, settings can be found in the <a href="#assembly">Assembly hub "genome" settings</a> section below.</p> <h3 id="useOneFile">Use <b><code>useOneFile on</code></b> for hubs with only one genome</h3> <p> If your hub is only displaying one genome, one can use the <a target="_blank" href="../hgTracksHelp.html#UseOneFile"><code>useOneFile on</code></a> setting to put all hub, genome, and track configuration settings into a single file. Load a working example <a target="_blank" href="../examples/hubExamples/hubUseOneFile/singleFileHubExample.txt">here</a>.</p> <h3 id="trackDb_txt">Declaring track settings</h3> <P>This document describes how to set dataset display characteristics using "track database" or "trackDb" settings through name-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. These stanzas should be structured according to the following format specification: <ul> <li>Lines consist of name-value pairs. The first line of the stanza establishes the <code>track</code> name. Additional lines will contain further "setting" names followed by "values" of one or more words of numbers. <li>All trackDb stanzas must begin with a <code>track</code> line and a stanza ends with a blank line. <li>Periods should be avoided in <code>track</code> names, although there are some settings that include periods in the name, e.g. filter.fieldName. <li>The format supports '\' continuation characters. If the setting is long or complex, break it into several lines using terminating '\' characters to make it more readable. <li>Text should be ASCII characters, but a limited set of Unicode characters are <a href="/FAQ/FAQcustom.html#custom13">supported for longLabel and shortLabel settings</a>. </ul> <p>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> Running hubCheck on your <code>hub.txt</code> file identifies errors in settings, file paths, and formatting that could prevent your hub from loading correctly. Download hubCheck from the <a href="https://hgdownload.soe.ucsc.edu/admin/exe/">utilities download page</a> and see the <a href="/goldenPath/help/hgTrackHubHelp.html#Compatibility">hubCheck documentation</a> and 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> for more information on validating hubs.</p> <h3 id="includes">Using trackDb include statements</h3> <p> Hubs also support the use of <a href="../hgTrackHubHelp.html#Includes">include statements</a>, allowing one to insert a file containing a set of trackDb stanzas into a primary trackDb. Use this when you have the same track across several assemblies, or several large, complex tracks. <h3 id="assembly_hubs">Assembly Hubs</h3> <p> Assembly hubs can display novel genome assemblies and annotations in the UCSC Genome Browser. Note: Many genome assemblies available in GenBank are also available in our <a href="https://hgdownload.gi.ucsc.edu/hubs" target="_blank">GenArk archive</a>. However, if your genome is not available in GenBank, you can make a custom assembly hub. To create an assembly hub, refer to our <a href="../assemblyHubUserGuide.html" target="_blank">Assembly Hub User Guide</a> or our <a href="../hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a>.</p> <h3 id="includes">Page Contents</h3> <P>The remainder of this document is divided into the following sections and should be used as a ready reference. Settings are colored based on their support level: <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>See the <a href="changes.html">list of changes</a> to see recent additions. </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>: Multiple 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> <LI><A HREF="#faceted_composite">Faceted Composites</A></LI> </UL></LI> <LI><A HREF="#aggregate">Aggregate or Overlay Tracks: multiWig</A></LI> </UL></LI> <LI><A HREF="#generalHubSettings">General Hub and Assembly Configuration Settings</A> <UL> <LI><A HREF="#hubGeneral">General hub configuration settings</A></LI> <LI><A HREF="#assembly">Assembly hub "genome" settings</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="singleCellColumnNames"><a name="singleCellColumnNames"></a> <img class='toggle detail'> <div class="format"><code class="level-new"> singleCellColumnNames off</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="style"><A name="style"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">style <heatmap></code></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 targetDb</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 valign=top><td class="hicArcLimit"><a name="hicArcLimit"></a><img class='toggle detail'> <div class="format"><code class="level-new">hicArcLimit <integer></code></div> </td></tr> <tr valign=top><td class="hicArcLimitEnabled"><a name="hicArcLimitEnabled"></a><img class='toggle detail'> <div class="format"><code class="level-new">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="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> <TR class="examples" VALIGN=TOP><TD class="view_exampleTwo"><IMG class='toggle detail'> <div class="format"><B>Example hub of a superTrack with a composite track containing different track types with Views</B></div> </TD></TR> </TABLE> <BR><BR> <A name="faceted_composite"></A> <TABLE class="settingsTable" id="Faceted_Composite_Settings"> <THEAD><TR><TD><DIV ID="faceted_composite_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Faceted composite track settings </TH></TR> <TR VALIGN=TOP><TD class="faceted"><IMG class='toggle detail'> <div class="format"><code>compositeTrack faceted</code></div> </TD></TR> <TR VALIGN=TOP><TD class="metaDataUrl"> <A name="metaDataUrl"></A><IMG class='toggle detail'> <div class="format"><code>metaDataUrl <url></code></div> </TD></TR> <TR VALIGN=TOP><TD class="primaryKey"> - <A name="metaDataUrl"></A><IMG class='toggle detail'> + <A name="primaryKey"></A><IMG class='toggle detail'> <div class="format"><code>primaryKey <field></code></div> </TD></TR> <TR VALIGN=TOP><TD class="maxCheckBoxes"><IMG class='toggle detail'> <div class="format"><code>maxCheckBoxes <integer></code></div> </TD></TR> <TR VALIGN=TOP><TD class="dataTypes"> <A name="dataTypes"></A><IMG class='toggle detail'> <div class="format"><code>dataTypes <name1|"table title" name2|"table title" ...></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="faceted_example1"> <IMG class='toggle detail'> <div class="format"><B>Example of a faceted composite track containing different track types:</B></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="faceted_example2"> <IMG class='toggle detail'> <div class="format"><B>Example of a faceted composite track containing different track samples and data types:</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> <!-- Next section --> <div class="contentBorder"> <A name="generalHubSettings"></A> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> General Hub and Assembly Configuration Settings</div> </div> <div class="borderGuard"> <p> This section describes hub and assembly configuration settings. It is recommended to use the <code>useOneFile</code> setting, which allows all hub configuration settings to be placed in a single file without the need for separate <code>hub.txt</code>, <code>genomes.txt</code>, or <code>trackDb.txt</code> files.</p> <A name="hubGeneral"></A> <TABLE class="settingsTable" id="general_hub_file_settings"> <THEAD><TR><TD><DIV ID="hub_general_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> General hub configuration settings </TH></TR> <TR VALIGN=TOP><TD class="hub"><IMG class='toggle detail'> <div class="format"><code class="level-base">hub <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="hubShortLabel"><IMG class='toggle detail'> <div class="format"><code class="level-base">shortLabel <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="hubLongLabel"><IMG class='toggle detail'> <div class="format"><code class="level-base">longLabel <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="genomesFile"><IMG class='toggle detail'> <div class="format"><code class="level-base">genomesFile <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="email"><IMG class='toggle detail'> <div class="format"><code class="level-base">email <email address></code></div> </TD></TR> <TR VALIGN=TOP><TD class="descriptionUrl"><IMG class='toggle detail'> <div class="format"><code class="level-base">descriptionUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="useOneFile"><IMG class='toggle detail'> <div class="format"><code class="level-base">useOneFile <on></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="hub_txt_example"> <IMG class='toggle detail'> <div class="format"><B>Example of an opening hub stanza</B></div> </TD></TR> </TABLE> <BR><BR> <A name="assembly"></A> <TABLE class="settingsTable" id="genomes_file_settings"> <THEAD><TR><TD><DIV ID="genomes_file_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Assembly hub "genome" settings </TH></TR> <TR VALIGN=TOP><TD class="genome"><IMG class='toggle detail'> <div class="format"><code class="level-base">genome <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="trackDbFile"><IMG class='toggle detail'> <div class="format"><code class="level-base">trackDb <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="groupsFile"><IMG class='toggle detail'> <div class="format"><code class="level-base">groups <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="description"><IMG class='toggle detail'> <div class="format"><code class="level-base">description <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="twoBitPath"><IMG class='toggle detail'> <div class="format"><code class="level-base">twoBitPath <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromAlias"><IMG class='toggle detail'> <div class="format"><code class="level-base">chromAlias <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromAliasBb"><IMG class='toggle detail'> <div class="format"><code class="level-base">chromAliasBb <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromSizes"><IMG class='toggle detail'> <div class="format"><code class="level-base">chromSizes <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="chromAuthority"><IMG class='toggle detail'> <div class="format"><code class="level-base">chromAuthority <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="organism"><IMG class='toggle detail'> <div class="format"><code class="level-base">organism <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultPos"><IMG class='toggle detail'> <div class="format"><code class="level-base">defaultPos <chr:start-end></code></div> </TD></TR> <TR VALIGN=TOP><TD class="orderKey"><IMG class='toggle detail'> <div class="format"><code class="level-base">orderKey <int></code></div> </TD></TR> <TR VALIGN=TOP><TD class="scientificName"><IMG class='toggle detail'> <div class="format"><code class="level-base">scientificName <str></code></div> </TD></TR> <TR VALIGN=TOP><TD class="htmlPath"><IMG class='toggle detail'> <div class="format"><code class="level-base">htmlPath <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="transBlat"><IMG class='toggle detail'> <div class="format"><code class="level-base">transBlat <url> <port></code></div> </TD></TR> <TR VALIGN=TOP><TD class="blat"><IMG class='toggle detail'> <div class="format"><code class="level-base">blat <url> <port></code></div> </TD></TR> <TR VALIGN=TOP><TD class="isPcr"><IMG class='toggle detail'> <div class="format"><code class="level-base">isPcr <url> <port></code></div> </TD></TR> <TR class="examples" VALIGN=TOP><TD class="genome_example"> <IMG class='toggle detail'> <div class="format"><B>Example of a genome stanza</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> 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