acf20930c5cdfa1e352826a702ad8f36344178c4
markd
  Thu Sep 24 21:16:13 2026 -0700
Fixes from an independent review of the TSS tracks. refs #35528

The Data Access sections told users to pass the composite name to the API, which
returns HTTP 400. The API serves one bigWig at a time, so both pages now name a
single strand of one cell line, verified to return 200.

encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files
went into each track, and it did not. Commit that manifest as
proCapNetEncodeFiles.tsv and name it on the page. It matters because
proCapNetEncodeMeta resolves each experiment's default analysis at run time, so
re-running it after an ENCODE reprocessing can pick different files.

Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap
experiments come from. Sagar Shah was credited by name with no reference.

The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on
the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each
gap, dropped because most of its 2114 bp window was unresolved.

diff --git src/hg/makeDb/trackDb/human/proCapNet.html src/hg/makeDb/trackDb/human/proCapNet.html
index d6a142ad6e7..6ea55a46079 100644
--- src/hg/makeDb/trackDb/human/proCapNet.html
+++ src/hg/makeDb/trackDb/human/proCapNet.html
@@ -133,31 +133,33 @@
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/$db/transcriptionStart.txt"
 target="_blank">doc/$db/transcriptionStart.txt</a>, the scripts they run are in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet"
 target="_blank">makeDb/outside/proCapNet</a>, and the track configuration is in
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/$db/transcriptionStart.ra"
 target="_blank">trackDb/human/$db/transcriptionStart.ra</a>.
 </p>
 
 <h2>Data Access</h2>
 
 <p>
 The data can be explored interactively in table format with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to
 spreadsheet or tab-sep tables. From scripts, the data can be accessed through our
-<a href="https://api.genome.ucsc.edu" target="_blank">API</a>, track=<i>proCapNet</i>.
+<a href="https://api.genome.ucsc.edu" target="_blank">API</a>. The API returns one
+bigWig at a time, so name a single strand of one cell line rather than the
+container, for example track=<i>proCapNet_K562_pred_pos</i>.
 </p>
 
 <p>
 The Files column of the table on this page links each cell line's bigWigs
 directly, so a single file can be fetched without working out its path.
 </p>
 
 <p>
 For automated download and analysis, the genome annotation is stored in bigWig
 files that can be downloaded from
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/proCapNet/" target="_blank">our
 download server</a>. Predictions are under <tt>pred/</tt> and are named for the
 cell line, the model and the strand, for example
 <tt>K562.proCapNet.pos.bw</tt> and <tt>K562.proCapNet.neg.bw</tt>. Contribution
 scores, which exist for GRCh38 only, are under <tt>contrib/</tt>, for example