66604eefdbb0971ed43ee81bd6f18cc3a409e304
markd
  Sat Jan 10 13:18:44 2026 -0800
color-code clsLongReadRna modles (#36908)

diff --git src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
index c85bacfc9ea..9e26b122a96 100644
--- src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
+++ src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
@@ -10,39 +10,54 @@
   Portions of this dataset were used to develop the lncRNA annotations
   introduced in GENCODE v47. The data are a superset of the data incorporated
   into GENCODE. The transcript models for a given RNA do not necessarily match
   those in GENCODE and are provided as a guide to exploring the sequencing data.
 </p>
 
 <p>
 Detailed descriptions of the data are available at the
 <a href="https://github.com/guigolab/CLS3_GENCODE" target="_blank">GENCODE CLS Project</a> site.</p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 This is a multi-view composite track containing multiple data types (views). Each view includes subtracks that are displayed individually in the browser. Instructions for configuring multi-view tracks are 
 <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.<br><br>
 
+
 <b>Views:</b><br>
 <ul>
   <li><b>Targets:</b> Capture target regions</li>
   <li><b>Models:</b> Transcript models generated from reads and merging</li>
   <li><b>Sample models:</b> Transcript models by sample in which they were observed </li>
   <li><b>Per-experiment reads:</b> Read mappings per experiment</li>
   <li><b>Per-experiment Models:</b> Transcript models generated from the experiments</li>
 </ul></p>
 
+<p><b>Model Color Coding</b> <br>
+<p>
+Model annotations are color-coded based on their incorporation into GENCODE V47
+and the assigned GENCODE V47 BioType:
+</p>
+<ul>
+  <li style="color: rgb(12,12,120);"><b>coding</b></li>
+  <li style="color: rgb(0,100,0);"><b>non-coding</b></li>
+  <li style="color: rgb(255,51,255);"><b>pseudogene</b></li>
+  <li style="color: rgb(254,0,0);"><b>to be experimentally confirmed (TEC)</b></li>
+  <li style="color: rgb(255,160,122);"><b>Not incorporated into GENCODE V47</b></li>
+</ul>
+
+
 <h2>Methods</h2>
 <p>
 This project, led by the 
 <a href="https://www.gencodegenes.org/" target="_blank">GENCODE consortium</a>,
 employed the Capture Long-read Sequencing (CLS) protocol to enrich transcripts from targeted genomic regions. It used a large capture array with orthologous probes in human and mouse genomes, targeting non-GENCODE lncRNA annotations and regions suspected of unannotated transcription. CapTrap-Seq, a cDNA library preparation protocol, was used to enrich for full-length RNA molecules (5′ to 3′).
 </p>
 
 <p>
 Matched adult and embryonic tissues from human and mouse were selected to maximize transcriptome complexity. Libraries were sequenced pre- and post-capture using PacBio and Oxford Nanopore Technologies (ONT) long-read platforms, as well as short-read technologies.
 </p>
 
 <p>
 Transcript isoform models were built from reads using the LyRic analysis software. These were merged using intron chains, with transcription start and end sites anchored using CAGE and poly(A) data.
 </p>