17b7d3c37be41135afaf8e91e365e3847af96ca5
lrnassar
  Mon Jun 22 10:56:56 2026 -0700
Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599

New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra
alpha in each assembly's trackDb.ra.

hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra
2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples),
and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets).
hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur).
mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE
(faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted
from mm10, lift noted in the long labels.

Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into
/gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under
makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch
for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt,
doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 0c38157241a..e3c5eef2820 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -36044,15 +36044,54 @@
 
 wigToBigWig a.wig /hive/data/genomes/hg19/chrom.sizes a.bw &
 wigToBigWig c.wig /hive/data/genomes/hg19/chrom.sizes c.bw &
 wigToBigWig g.wig /hive/data/genomes/hg19/chrom.sizes g.bw &
 wigToBigWig t.wig /hive/data/genomes/hg19/chrom.sizes t.bw &
 wait
 rm -f *.wig
 
 # Color overlays generated with:
 ~/kent/src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
 
 # Install to /gbdb:
 mkdir -p /gbdb/hg19/clinPred
 ln -s /hive/data/genomes/hg19/bed/clinPred/{a,c,g,t}.bw /gbdb/hg19/clinPred/
 ln -s /hive/data/genomes/hg19/bed/clinPred/{a,c,g,t}.color.bb /gbdb/hg19/clinPred/
+
+
+# hg19 TADs supertrack (tads) - Redmine #21599
+# hg19 carries the three sources that have hg19-compatible data: Dixon 2012 (domains),
+# Schmitt 2016 (boundaries), McArthur & Capra 2021 (boundary stability). ENCODE contact
+# domains and the 3D Genome Browser collection are hg38-only (not on hg19).
+# Data built 2026-06-14 alongside hg38 (same source files, autoSql, conventions). Full source
+# provenance + fetch for each dataset is in ../hg38/tad.txt (Dixon MOESM330 suppl; Schmitt
+# mmc4.xlsx manual; McArthur
+# GitHub byStability.bed). hg19 differs from hg38 only in the liftOver target:
+
+##############################################################################
+# Dixon 2012 TAD domains (tadsDixon) - hESC + IMR90, lifted hg18 -> hg19
+##############################################################################
+# Nature suppl Table S3 "Combined" sheets (hESC/IMR90, hg18, BED3) staged at
+# /hive/data/outside/tad/dixon2012/source/dixon_{hESC,IMR90}.hg18.bed (name=cell type).
+# liftOver hg18->hg19 (hg18ToHg19.over.chain), bedClip, primary-chrom filter, sort,
+# bedToBigBed -type=bed4 -as=tadDomain.as -> build/hg19/tadsDixon{HESC,IMR90}.bb (HESC 3,062).
+
+##############################################################################
+# Schmitt 2016 TAD boundaries (tadsSchmitt) - 21 samples, NATIVE hg19 (no lift)
+##############################################################################
+# Cell Reports suppl Table S3 (mmc4.xlsx, manual download), 21 per-sample sheets, 40 kb bins,
+# hg19 -> source/schmitt_<code>.hg19.bed. bedToBigBed -type=bed4 -as=tadBoundary.as ->
+# build/hg19/tadsSchmitt<code>.bb (21 files; native hg19, no liftOver).
+
+##############################################################################
+# McArthur 2021 TAD boundary stability (tadsMcArthur) - NATIVE hg19 (no lift)
+##############################################################################
+# GitHub emcarthur/TAD-stability-heritability, 100kbBookendBoundaries_byStability.bed (hg19,
+# 14,345 boundaries, 100 kb; cols chr loc loc2 counts percentile). Drop header, bedToBigBed
+# -type=bed5+2 -as=tadStability.as -> build/hg19/tadsMcArthur.bb (14,344). bed5+2: name,
+# score=round(contexts/37*1000) (render proxy), contexts (1-37), percentile.
+
+# gbdb: /gbdb/hg19/bbi/tad/{tadsDixon*,tadsSchmitt*,tadsMcArthur}.bb (symlinks to build/hg19/).
+# trackDb: human/hg19/tad.ra (priorities Dixon 1 / Schmitt 2 / McArthur 3; superTrack on hide;
+#   Dixon visibility pack, Schmitt+McArthur hide) + tads/tadsDixon/tadsSchmitt/tadsMcArthur .html.
+#   Gated: include tad.ra alpha in human/hg19/trackDb.ra.
+cd ~/kent/src/hg/makeDb/trackDb && make DBS=hg19 FIND=find