0f951bfc96241a7362d1512ceecf59a02682a839
markd
  Thu Sep 24 20:40:52 2026 -0700
Description page fixes from a QA pre-pass on the TSS tracks. refs #35528

Encode the non-ASCII character in the Avsec reference on proCapNet.html.
getTrackReferences emits raw UTF-8, which the browser does not transcode.

Use $db rather than a hardcoded hg38 in the proCapNet download-server link and
the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader
was being pointed at hg38 files.

Add a Source subsection to proCapNet.html linking the makedoc, the build scripts,
the trackDb file and the upstream kundajelab/ProCapNet repository. These links
went missing when the Processing at UCSC section was dropped; the prose stays
dropped.

Drop the cross-links between the two track pages. Track names are prefixed
hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a
bare-name link cannot work there. Each page now states which assemblies the data
is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1.

Bold the two UI control names on the proCapNet display conventions section.

diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html
index bc9dbff8ba0..4456dffb38e 100644
--- src/hg/makeDb/trackDb/human/encode4ProCap.html
+++ src/hg/makeDb/trackDb/human/encode4ProCap.html
@@ -1,32 +1,33 @@
 <h2>Description</h2>
 
 <p>
 Transcription begins when RNA polymerase II starts making an RNA at a
 transcription start site. A promoter or an enhancer does not use a single start
 site: polymerase initiates across a spread of nearby bases, on both strands, and
 which bases are used is set largely by the local DNA sequence. PRO-cap is a
 nascent RNA run-on assay that captures the 5' end of each new transcript, so each
 read reports the exact base and strand of one initiation event. Unlike RNA-seq or
 CAGE, PRO-cap sees unstable RNAs as well as stable ones, which makes initiation
 at enhancers visible.
 </p>
 
 <p>
-This track shows PRO-cap signal from six ENCODE 4 experiments, one per cell line.
-The predictions a deep learning model makes from sequence alone, trained on this
-same data, are in the <a href="hgTrackUi?g=proCapNet">ProCapNet</a> track.
+This track shows PRO-cap signal from six ENCODE 4 experiments, one per cell line,
+on GRCh38/hg38 only. The predictions a deep learning model makes from sequence
+alone, trained on this same data, are in the ProCapNet track, available on
+GRCh38/hg38 and T2T-CHM13/hs1.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 Cell lines are listed in the table on this page, one row each. Use the Sample
 class facet to narrow the list, and the Experiment column to open the experiment
 on the ENCODE portal.
 </p>
 
 <p>
 Each track is an overlay of the two strands: plus strand reads are drawn upward
 and minus strand reads downward. The y axis is the number of initiation events
 measured at that base, summed over the experiment's replicates, so tracks with
 deeper sequencing reach higher values. Tracks are colored by cell line: