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/trackDb/mouse/mm39/tad.ra src/hg/makeDb/trackDb/mouse/mm39/tad.ra
new file mode 100644
index 00000000000..4aee4acea70
--- /dev/null
+++ src/hg/makeDb/trackDb/mouse/mm39/tad.ra
@@ -0,0 +1,39 @@
+track tads
+superTrack on hide
+shortLabel TADs
+longLabel Topologically associating domains (TADs) from Hi-C studies
+group regulation
+html tads
+
+track tadsDixon
+parent tads
+priority 1
+compositeTrack on
+shortLabel Dixon 2012 TADs
+longLabel TAD domains in mESC and cortex (Dixon et al. 2012, lifted from mm9)
+type bigBed 4
+group regulation
+visibility pack
+html tadsDixon
+
+    track tadsDixonMESC
+    parent tadsDixon on
+    shortLabel mESC TADs
+    longLabel TAD domains in mouse embryonic stem cells (Dixon et al. 2012, lifted from mm9)
+    type bigBed 4
+    bigDataUrl /gbdb/$D/bbi/tad/tadsDixonMESC.bb
+    color 27,158,119
+    mouseOver Cell type: $name (TAD domain)
+
+    track tadsDixonCortex
+    parent tadsDixon on
+    shortLabel Cortex TADs
+    longLabel TAD domains in mouse cortex (Dixon et al. 2012, lifted from mm9)
+    type bigBed 4
+    bigDataUrl /gbdb/$D/bbi/tad/tadsDixonCortex.bb
+    color 106,61,154
+    mouseOver Cell type: $name (TAD domain)
+
+include tadsEncode.ra
+
+include tads3dgb.ra