4e986673a37800eacf1d36309b0cd38564a4bb1f
max
  Wed Mar 25 07:55:59 2026 -0700
PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/promoterAi.txt src/hg/makeDb/doc/hg38/promoterAi.txt
new file mode 100644
index 00000000000..33de0152e1f
--- /dev/null
+++ src/hg/makeDb/doc/hg38/promoterAi.txt
@@ -0,0 +1,32 @@
+# PromoterAI, Claude max, Mar 20 2026
+
+# Source: promoterAI_tss500.tsv.gz from https://primateai3d.basespace.illumina.com/
+# 262M rows, 118.6M unique variants, 39.5M unique positions, scores within 500bp of TSS
+
+cd /hive/data/genomes/hg38/bed/promoterai
+# download promoterAI_tss500.tsv.gz from Illumina BaseSpace (requires registration)
+
+# convert to 4 bedGraph files (one per alt allele) + overlap BED
+# picks max absolute score when transcripts overlap; overlap BED has all per-transcript scores
+python3 ~/kent/src/hg/makeDb/scripts/promoterAiToBigWig.py
+
+# sort bedGraphs and convert to bigWig
+for alt in A C G T; do
+    sort -k1,1 -k2,2n promoterAi_${alt}.bedGraph > promoterAi_${alt}.sorted.bedGraph
+    bedGraphToBigWig promoterAi_${alt}.sorted.bedGraph /hive/data/genomes/hg38/chrom.sizes promoterAi_${alt}.bw
+    rm promoterAi_${alt}.bedGraph promoterAi_${alt}.sorted.bedGraph
+done
+
+# sort overlap BED and convert to bigBed
+sort -k1,1 -k2,2n promoterAi_overlaps.bed > promoterAi_overlaps.sorted.bed
+bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/promoterAiOverlaps.as -tab \
+    promoterAi_overlaps.sorted.bed /hive/data/genomes/hg38/chrom.sizes promoterAi_overlaps.bb
+rm promoterAi_overlaps.bed promoterAi_overlaps.sorted.bed
+
+# symlinks
+mkdir -p /gbdb/hg38/promoterAi
+ln -s /hive/data/genomes/hg38/bed/promoterai/promoterAi_A.bw /gbdb/hg38/promoterAi/a.bw
+ln -s /hive/data/genomes/hg38/bed/promoterai/promoterAi_C.bw /gbdb/hg38/promoterAi/c.bw
+ln -s /hive/data/genomes/hg38/bed/promoterai/promoterAi_G.bw /gbdb/hg38/promoterAi/g.bw
+ln -s /hive/data/genomes/hg38/bed/promoterai/promoterAi_T.bw /gbdb/hg38/promoterAi/t.bw
+ln -s /hive/data/genomes/hg38/bed/promoterai/promoterAi_overlaps.bb /gbdb/hg38/promoterAi/overlaps.bb