9af4842cd888f9150257834edb17991f7a2ae697 gperez2 Mon Dec 9 11:49:34 2024 -0800 Added a FAQ entry for SuperTracks vs composite tracks, refs #28196 diff --git src/hg/htdocs/FAQ/FAQtracks.html src/hg/htdocs/FAQ/FAQtracks.html index 2849b7a..8602f01 100755 --- src/hg/htdocs/FAQ/FAQtracks.html +++ src/hg/htdocs/FAQ/FAQtracks.html @@ -19,30 +19,31 @@ <li><a href="#tracks4">Position changes of features</a></li> <li><a href="#tracks6">Evaluating possible alternative splices</a></li> <li><a href="#tracks7">Matching exons and protein sequence</a></li> <li><a href="#tracks9">Cause of duplicated gene</a></li> <li><a href="#tracks11">Protein doesn't begin with methionine</a></li> <li><a href="#tracks12">Doing an orthology track analysis of a protein</a></li> <li><a href="#tracks14">Quality benchmarks for predicted genes</a></li> <li><a href="#tracks15">Display conventions for gene prediction tracks</a></li> <li><a href="#tracks16">Viewing detailed displays in conservation tracks</a></li> <li><a href="#tracks17">Negative strand coordinates in PSL files</a></li> <li><a href="#tracks18">Inconsistency in stop codon treatment in GTF tracks</a></li> <li><a href="#tracks19">Obtaining clones referenced in Genome Browser</a></li> <li><a href="#tracks20">Locating centromeres and telomeres</a></li> <li><a href="#tracks21">Determining the table name for an annotation track</a></li> <li><a href="#tracks22">Unexpected results in UCSC RefSeq track</a></li> +<li><a href="#tracks23">What is the difference between super tracks and composite tracks?</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="speed"></a> <h2>Why is my tracks display slow?</h2> <p> There are different reasons why the Genome Browser tracks display can become slow. Below is a list of common scenarios alongside potential solutions. The most common reason involves the configuration settings that are saved as users interact with the Genome Browser, such as track visibilities and custom data. This can be solved by a reset of all your current Genome Browser session information although it is important to note that this will reset all settings including filters, track order and remove all custom data. To do @@ -418,16 +419,80 @@ <p> In 2017, NCBI RefSeq coordinates for hg38 were used for generating non-discrepant RefSeq tracks in the UCSC Genome Browser. This new <a href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite" target="_blank">NCBI RefSeq track</a> in the UCSC Genome Browser displays identical RNA coordinates to annotations in the <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">NCBI Reference Sequence Database</a>. Please note that when annotations do map to multiple loci, the NCBI RefSeq track displays unique identifiers for each locus, while the UCSC RefSeq track retains the same identifier.</p> <p> For more information and future plans to integrate coordinate-generated NCBI RefSeq tracks for other assemblies, please see the <a href="https://genome-blog.gi.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/" target="_blank">NCBI RefSeq track blog post</a>.</p> +<a name="tracks23"></a> +<h2>SuperTracks vs composite tracks</h2> +<h6>What is the difference between superTracks and composite tracks?</h6> +<p><b>Composite Tracks</b>:</p> +<ul> + <li>Group related tracks (subtracks) under a single parent, typically of similar data type but they can + have <a href="../goldenPath/help/trackDb/trackDbHub.html#subGroups" target="_blank">subGroups</a> + and <a href="../goldenPath/help/trackDb/trackDbHub.html#view" target="_blank">views</a>. + Views allow mixing different data types (bigBeds and bigWigs).</li> + <li>Use <code>compositeTrack on</code> to define the parent track. Subtracks reference the parent using + <code>parent compositeTrackName [on/off]</code> to control their default visibility.</li> + <li>Certain configuration settings can be applied across all subtracks within a composite, such as + color schemes, visibility, and labels can be defined at the composite track (parent) level + and inherited by all its subtracks (children). This ensures consistency and simplifies + management by reducing redundancy, as you don't need to define the same settings repeatedly + for each subtrack.</li> +</ul> +<p>Basic Structure: +<pre><code>track compositeTrackName +compositeTrack on +... + track subTrack_1_Name + parent compositeTrackName on + ... + track subTrack_2_Name + parent compositeTrackName off +</code></pre></p> +<p><b>Supertracks</b>:</p> +<p> +<ul> + <li>Organize diverse tracks, including composite tracks, into a high-level hierarchy. + Supertracks offer flexibility to group a variety of track types, not limited to similar data + types, and support two levels of hierarchy for complex nesting (e.g., supertrack → composite → subtrack).</li> + <li>Declared with <code>superTrack on show</code>, where <code>show</code> is optional and determines default visibility.</li> + <li>Subtracks reference the parent supertrack using <code>parent superTrackName</code> and do not follow the parent + line directly, as composite tracks do (e.g., <code>parent superTrackName <s>[on/off]</s></code>). Subtrack + (children) must explicitly define their visibility settings (dense, hide, etc.) unless the default hide is + acceptable.</li> +</ul> +<p>Basic Structure: +<pre><code>track superTrackName +superTrack on show +... + track subTrackNameInSuperTrack + parent superTrackName + ... + track compositeTrackNameInSuperTrack + compositeTrack on + parent superTrackName + ... + track subTrack_1_NameIncomposite + parent compositeTrackNameInSuperTrack on + ... + track subTrack_2_NameIncomposite + parent compositeTrackNameInSuperTrack off +</code></pre></p> +<p><b>Key Differences</b>:</p> +<ul> + <li>Composite Tracks: Group similar subtracks in a single level with visibility set per track using [on/off].</li> + <li>Supertracks: Group diverse tracks (including composite tracks) in a two level of hierarchy with visibility set + separately for each subtrack.</li> +</ul> +<p>For more information about superTracks and composite tracks, refer to the +<a href="../goldenPath/help/hubQuickStartGroups" target="_blank">Organizing Track Hubs into Groupings help page</a>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->