cf59add626c31740a9a65a4c576b71b822260ced
max
  Tue Mar 24 04:18:15 2026 -0700
fixing up NMD track and adding decorator tdb, refs #33737

diff --git src/hg/makeDb/doc/hg38/nmd.txt src/hg/makeDb/doc/hg38/nmd.txt
index 064f8ee719c..10cc23c8fc4 100644
--- src/hg/makeDb/doc/hg38/nmd.txt
+++ src/hg/makeDb/doc/hg38/nmd.txt
@@ -1,51 +1,53 @@
 #######################################################################
 # NMD escape regions from Gencode (2025-03-24 max/Claude)
 # Two outputs: decorator bigBed (per-transcript) and collapsed bigBed (merged by coordinates)
 # Collapsed version uses gene symbols from input, colors by rule, transcript lists
 # Script accepts -f bigGenePred (gencode .bb) or -f genePredExt (ncbiRefSeq .txt.gz)
 
 cd /hive/data/genomes/hg38/bed/nmd/gencode/
 
 # run the script on gencode bigGenePred - produces decorator + collapsed BED files
 ~/kent/src/hg/makeDb/scripts/nmd/genePredNmdEsc -f bigGenePred \
     /hive/data/genomes/hg38/bed/gencodeV49/build/hg38.gencodeV49.bb \
-    knownGeneNmdProt.bed nmdEscRegions.bed
+    knownGeneNmdDeco.bed nmdEscRegions.bed
 
 # build decorator bigBed
-bedSort knownGeneNmdProt.bed knownGeneNmdProt.bed
-bedToBigBed knownGeneNmdProt.bed ../../../chrom.sizes knownGeneNmdProt.bb \
+bedSort knownGeneNmdDeco.bed knownGeneNmdDeco.bed
+bedToBigBed knownGeneNmdDeco.bed ../../../chrom.sizes knownGeneNmdDeco.bb \
     -tab -type=bed12+5 -as=${HOME}/kent/src/hg/makeDb/scripts/nmd/nmdEscDecoration.as
 
 # build collapsed bigBed
 bedSort nmdEscRegions.bed nmdEscRegions.bed
 bedToBigBed nmdEscRegions.bed ../../../chrom.sizes nmdEscRegions.bb \
     -tab -type=bed9+2 -as=${HOME}/kent/src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as
 
 
 #######################################################################
 # NMD escape regions from NCBI RefSeq (2025-03-24 max)
 
 cd /hive/data/genomes/hg38/bed/nmd/ncbiRefSeq/
 
 # run the script on ncbiRefSeq genePredExt
 # Using all of RefSeq, not just refseq curated - good idea?
 # This is the file for RefSeq curated: /hive/data/genomes/hg38/bed/ncbiRefSeq.p14.2025-08-13/archive/hg38.ncbiRefSeqCurated.txt.gz 
 ~/kent/src/hg/makeDb/scripts/nmd/genePredNmdEsc -f genePredExt \
     /hive/data/genomes/hg38/bed/ncbiRefSeq.p14.2025-08-13/archive/hg38.ncbiRefSeq.txt.gz
     nmdNcbiRefSeqDeco.bed nmdEscNcbiRefSeq.bed
 
+# not building decorator file - needed? Useful?
+
 # build collapsed bigBed
 bedSort nmdEscNcbiRefSeq.bed nmdEscNcbiRefSeq.bed
 bedToBigBed nmdEscNcbiRefSeq.bed ../../../chrom.sizes nmdEscNcbiRefSeq.bb \
     -tab -type=bed9+2 -as=${HOME}/kent/src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as
 
 # symlink to gbdb
 ln -sf /hive/data/genomes/hg38/bed/nmd/ncbiRefSeq/nmdEscNcbiRefSeq.bb /gbdb/hg38/nmd/nmdEscNcbiRefSeq.bb
 
 #######################################################################
 # Lindeboom et al. NMDetective scores (2025-03-23 max/Claude)
 # NMD efficiency predictions from Lindeboom et al. 2019, Nat Genet.
 # Four bedGraph custom track files downloaded to:
 #   /hive/data/genomes/hg38/bed/nmd/lindeboom/
 # Data downloaded from https://figshare.com/articles/dataset/NMDetective/7803398
 # Custom track data in the session links from that page