bfa91627a224f0ca4a9e10718297df25f163847a
max
  Tue Mar 24 04:09:48 2026 -0700
adding NMD escape supertrack, refs #33737

diff --git src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh
new file mode 100755
index 00000000000..1f05d906d56
--- /dev/null
+++ src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+# Convert Lindeboom et al. NMDetective .ct (bedGraph custom track) files to bigWig
+# These are NMD efficiency predictions from Lindeboom et al. 2019, Nat Genet.
+
+set -beEu -o pipefail
+
+db=hg38
+inDir=/hive/data/genomes/$db/bed/nmd/lindeboom
+gbdbDir=/gbdb/$db/nmd
+chromSizes=/hive/data/genomes/$db/chrom.sizes
+
+mkdir -p $gbdbDir
+
+for ct in $inDir/*.ct; do
+    base=$(basename $ct .ct)
+    echo "Converting $base"
+    # strip the track header line then sort and convert
+    tail -n +2 $ct | sort -k1,1 -k2,2n > $inDir/$base.bedGraph
+    bedGraphToBigWig $inDir/$base.bedGraph $chromSizes $inDir/$base.bw
+    rm $inDir/$base.bedGraph
+    ln -sf $inDir/$base.bw $gbdbDir/$base.bw
+done
+
+echo "Done. bigWig files in $inDir, symlinked from $gbdbDir:"
+ls -l $gbdbDir/*.bw