4bd316f5f1ca47328bd3f9a181214b788055f0bc
lrnassar
  Tue Apr 21 13:29:26 2026 -0700
NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737

Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all)
to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models)
per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts".

Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of
len(cdsExons)==1. The old test misclassified multi-exon transcripts with a
single CDS exon (UTR introns) as "intronless" and silently suppressed their
Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated
and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt
both tracks.

Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a
penultimate coding exon shorter than 50 bp.

Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq.

QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links
given target="_blank" across all three HTML pages, dead commented nmdGencode
block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4
color and the gene-symbol-to-transcript-ID fallback.

Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.

diff --git src/hg/makeDb/trackDb/human/hg38/nmdDetective.html src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
index 571b8133cca..10bcc67b28a 100644
--- src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
+++ src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
@@ -76,32 +76,32 @@
 The predictions were generated for every possible PTC-introducing single-nucleotide
 variant and for the first out-of-frame PTC from every possible single-nucleotide
 frameshifting indel across all human protein-coding transcripts. The original bedGraph
 custom track files were downloaded from the
 <a href="https://figshare.com/articles/dataset/NMDetective/7803398" target="_blank">NMDetective Figshare page</a>
 resource and converted to bigWig format at UCSC.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The data underlying these tracks can be explored interactively with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis,
 the data may be queried from our
 <a href="/goldenPath/help/api.html">REST API</a>. Please refer to our
-<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing
-list archives</a> for questions, or our
+<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"
+target="_blank">mailing list archives</a> for questions, or our
 <a href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more
 information.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to Rik Lindeboom for providing custom tracks and the original NMDetective data
 on <a href="https://figshare.com/articles/dataset/NMDetective/7803398"
 target="_blank">Figshare</a>.
 </p>
 
 <h2>References</h2>
 
 <p>
 Lindeboom RG, Supek F, Lehner B.