9c0f52be6be34a120bd16008b57fc60728bd63bd
lrnassar
  Thu May 14 14:48:03 2026 -0700
Update ENCODE4 Regulation makedocs with note 141 QA follow-ups (H3K27ac color, metadata Organ casing, longLabel species prefix). refs #34923

diff --git src/hg/makeDb/doc/mm10.encode4.regulation.txt src/hg/makeDb/doc/mm10.encode4.regulation.txt
index e032deb1ea1..201770a4e23 100644
--- src/hg/makeDb/doc/mm10.encode4.regulation.txt
+++ src/hg/makeDb/doc/mm10.encode4.regulation.txt
@@ -311,15 +311,37 @@
 # ├── encode4RegAtac        (multiWig, hide)                         priority 1.2
 # ├── encode4RegMarkH3k4me3 (multiWig, hide)                         priority 1.3
 # ├── encode4RegMarkCtcf    (multiWig, hide)                         priority 1.5
 # ├── encode4RegTxn         (multiWig, hide)                         priority 1.6
 # ├── encode4RegEpigenetics (bigComposite faceted, 1,178, 30 ON)     priority 2.0
 # ├── encode4RegRnaSeq      (bigComposite faceted, 1,054, 6 ON)      priority 2.1
 # └── encode4RegTfChip      (bigComposite faceted, 334, 10 ON)       priority 2.2
 
 # Disk usage (/gbdb/mm10/encode4/regulation/):
 #   organAve:          1.5 TB (122 files)
 #   metadata + JSON:   ~1 MB (5 files)
 #   Total:             1.5 TB (128 files)
 #   (1 additional file: hub.txt reference copy)
 
 # File list: /hive/users/lrnassar/claude/RM34923/gbdb_file_list.txt
+
+##############################################################################
+# Internal QA follow-ups (Gerardo's note 141, 2026-05-14)
+##############################################################################
+
+# mm10 was already clean on the two assembly-specific issues raised in note
+# 141 (H3K27ac color was uniform 181,145,0; Organ-column casing in all three
+# metadata TSVs had no duplicates). The cross-assembly cleanup that did
+# touch mm10:
+
+# Fix C — Strip "Mus musculus " prefix from bigComposite longLabels.
+# All 2,566 mm10 bigComposite subtrack longLabels (1,178 Epi + 334 TfChip +
+# 1,054 RnaSeq) started with the species name. Stripped in commit 47519c28b9a
+# alongside the hg38 equivalent. See hg38/encode4.regulation.txt for full
+# context.
+
+cd ~/kent
+for f in src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra \
+         src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra \
+         src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra; do
+    sed -i 's/^\(\s*longLabel\) Mus musculus /\1 /' "$f"
+done