afbe6b6e1ac59c72526ce6515cca0abea576e9d9
max
  Wed Mar 25 02:01:33 2026 -0700
fix missing backslash and wrong year in nmd makedoc

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/nmd.txt src/hg/makeDb/doc/hg38/nmd.txt
index 10cc23c8fc4..ca02de5aac9 100644
--- src/hg/makeDb/doc/hg38/nmd.txt
+++ src/hg/makeDb/doc/hg38/nmd.txt
@@ -19,43 +19,43 @@
 # 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
+    /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.
+# NMD efficiency predictions from Lindeboom et al. 2016, 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
 # - NMDetectiveA.ct  - Random forest prediction of NMD efficiency
 # - NMDetectiveB.ct  - Decision tree prediction of NMD efficiency
 # - nmdDectA-ptc.ct  - Random forest, first out-of-frame PTC
 # - nmdDectB-ptc.ct  - Decision tree, first out-of-frame PTC
 
 # Convert bedGraph custom tracks to bigWig and symlink from /gbdb:
 cd /hive/data/genomes/hg38/bed/nmd/lindeboom/
 bash ~/kent/src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh