3a62ea7e9a8cb3503586a0a78570331308c9bc58
max
  Mon Apr 27 02:23:00 2026 -0700
NMD Escape MANE: expose NM_ accession via labelFields. refs #33737

Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default
instead of the HGNC gene symbol, with the ENST and gene symbol still
selectable via labelFields.

- genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused).
When set, the named bigGenePred column is captured per-transcript and
written into a new ncbiIds output column. For MANE pass 21.
- genePredNmdEsc: new --no-collapse option. By default, regions with
identical (chrom, start, end, rule) from multiple transcripts collapse
into one row with comma-separated lists. With --no-collapse the script
emits one row per (transcript, region). Used for MANE so each
label-field column holds a single value: the 74 MANE Plus Clinical
genes (e.g. LMNA) get two rows per region instead of one row with a
two-element list.
- nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3.
- nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts;
defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq
subtracks unchanged - they default to the gene symbol (name column)
and have an empty ncbiIds column.
- doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3
and document the --ncbi-id-field 21 + --no-collapse invocation for
MANE.

Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.

diff --git src/hg/makeDb/trackDb/human/hg38/nmd.ra src/hg/makeDb/trackDb/human/hg38/nmd.ra
index b7a9dc837c3..e6832f3c69f 100644
--- src/hg/makeDb/trackDb/human/hg38/nmd.ra
+++ src/hg/makeDb/trackDb/human/hg38/nmd.ra
@@ -4,33 +4,39 @@
 group genes
 type bed 4
 visibility hide
 superTrack on
 pennantIcon New red ../goldenPath/newsarch.html#042226 "Released Apr. 22, 2026"
 
         track nmdEscMane
         shortLabel NMD Escape MANE
         longLabel NMD escape predictions: MANE Select Plus Clinical transcripts
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdEscMane.bb
         visibility hide
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
+        labelFields ncbiIds,name,transcripts
+        defaultLabelFields ncbiIds
+        labelSeparator " / "
         filterText.transcripts *
         filterType.transcripts wildcard
-        filterLabel.transcripts Filter on transcript ID (e.g. "*ENST00000269305*")
+        filterLabel.transcripts Gencode accession (e.g. "*ENST00000269305*")
+        filterText.ncbiIds *
+        filterType.ncbiIds wildcard
+        filterLabel.ncbiIds RefSeq accession (e.g. "*NM_000546*")
         dataVersion MANE 1.5
         priority 1.4
 
         track nmdEscGencode
         shortLabel NMD Escape Gencode
         longLabel NMD escape predictions: Gencode transcripts
         parent nmd off
         bigDataUrl /gbdb/hg38/nmd/nmdEscRegions.bb
         visibility hide
         type bigBed 9 +
         mouseOverField mouseover
         html nmdEscTranscripts
         filterText.transcripts *
         filterType.transcripts wildcard
         filterLabel.transcripts Filter on transcript ID (e.g. "*ENST00000269305*")