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/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra
index f0b122a368e..754ef48affe 100644
--- src/hg/makeDb/trackDb/relatedTracks.ra
+++ src/hg/makeDb/trackDb/relatedTracks.ra
@@ -106,15 +106,21 @@
 
 # PrimateAI-3D cross-links:
 hg38 primateAi alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor
 hg38 alphaMissense primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation
 hg38 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors
 hg38 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure
 
 hg19 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors
 hg19 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure
 
 # PromoterAI cross-links:
 hg38 promoterAi primateAi PrimateAI-3D, a companion deep-learning model from Illumina for coding (missense) variants
 hg38 primateAi promoterAi PromoterAI, a companion deep-learning model from Illumina for non-coding promoter variants
 hg38 promoterAi alphaMissense AlphaMissense, a deep-learning predictor of missense (coding) variant pathogenicity
 hg38 alphaMissense promoterAi PromoterAI, a deep-learning predictor of expression-altering variants in promoter regions
+
+# NMD Escape cross-links:
+hg38 nmd mane MANE Select transcripts from NCBI/EBI, a curated subset of RefSeq/Ensembl transcripts used as clinical reference
+hg38 mane nmd NMD Escape: predicted regions where premature termination codons escape nonsense-mediated decay
+hg38 nmd ncbiRefSeq NCBI RefSeq transcripts, the source annotation set for the NMD Escape RefSeq subtrack
+hg38 ncbiRefSeq nmd NMD Escape: predicted regions where premature termination codons escape nonsense-mediated decay