fe4c75c272ca27de55c0b42396c47f2b00637a4a
jnavarr5
  Mon Sep 28 16:36:20 2026 -0700
Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528

diff --git src/hg/makeDb/trackDb/human/encode4ProCap.html src/hg/makeDb/trackDb/human/encode4ProCap.html
index 1a5f1b8a93c..e6831ba0819 100644
--- src/hg/makeDb/trackDb/human/encode4ProCap.html
+++ src/hg/makeDb/trackDb/human/encode4ProCap.html
@@ -57,35 +57,37 @@
 <p>
 The signal files were downloaded from the
 <a href="https://www.encodeproject.org" target="_blank">ENCODE portal</a>, taking
 only the plus and minus strand signal of unique reads belonging to each
 experiment's default analysis. ENCODE publishes no pooled file, so the
 per-replicate files were summed at UCSC into one track per cell line and strand,
 the same merge the ProCapNet models were trained on. Total signal is conserved
 exactly by the summing, and minus strand signal is negative as released. The
 experiments are ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR098LLB, ENCSR261KBX
 and ENCSR799DGV for A673, Caco-2, Calu3, HUVEC, K562 and MCF10A respectively.
 </p>
 
 <p>
 The steps are recorded in
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/transcriptionStart.txt"
-target="_blank">doc/hg38/transcriptionStart.txt</a> and the scripts are in
+target="_blank">doc/hg38/transcriptionStart.txt</a>, the scripts are in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet"
 target="_blank">makeDb/outside/proCapNet</a>, including
 <tt>proCapNetEncodeFiles.tsv</tt>, which records exactly which ENCODE file
-accessions went into each track.
+accessions went into each track, and the track configuration is in
+<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra"
+target="_blank">trackDb/human/hg38/transcriptionStart.ra</a>.
 </p>
 
 <h2>Data Access</h2>
 
 <p>
 The bigWig files are on our
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4ProCap/" target="_blank">download
 server</a>, named for the cell line, the ENCODE experiment accession and the
 strand, for example <tt>K562.ENCSR261KBX.pos.bw</tt> and
 <tt>K562.ENCSR261KBX.neg.bw</tt>.
 </p>
 
 <p>
 The data can be explored interactively in table format with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the