efebc8a0a29aeef60bc470a40ced7a2aa6652efd
lrnassar
  Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308

New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.

Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.

Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.

Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.ra src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.ra
new file mode 100644
index 00000000000..9f6e91fab79
--- /dev/null
+++ src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.ra
@@ -0,0 +1,20 @@
+track mouseStrainsCactus
+shortLabel Mouse Strain Alignments
+longLabel Cactus alignment of 16 mouse strains and rat
+type bigMaf
+group compGeno
+visibility hide
+priority 3
+color 0, 10, 100
+altColor 0,90,10
+bigDataUrl https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/mm10.bigMaf.bb
+summary https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/mm10.bigMafSummary.bb
+frames https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/mm10/maf/mm10.bigMafFrames.bb
+speciesCodonDefault mm10
+speciesGroups Wild_derived Classical_laboratory Rat/rn6
+sGroup_Wild_derived SPRET_EiJ PWK_PhJ CAST_EiJ WSB_EiJ
+sGroup_Classical_laboratory NZO_HlLtJ C57BL_6NJ NOD_ShiLtJ FVB_NJ DBA_2J CBA_J C3H_HeJ AKR_J BALB_cJ A_J LP_J 129S1_SvImJ
+sGroup_Rat/rn6 rn6
+speciesLabels SPRET_EiJ="SPRET/EiJ" PWK_PhJ="PWK/PhJ" CAST_EiJ="CAST/EiJ" WSB_EiJ="WSB/EiJ" NZO_HlLtJ="NZO/HlLtJ" C57BL_6NJ="C57BL/6NJ" NOD_ShiLtJ="NOD/ShiLtJ" FVB_NJ="FVB/NJ" DBA_2J="DBA/2J" CBA_J="CBA/J" C3H_HeJ="C3H/HeJ" AKR_J="AKR/J" BALB_cJ="BALB/cJ" A_J="A/J" LP_J="LP/J" 129S1_SvImJ="129S1/SvImJ" rn6="Rat/rn6"
+itemFirstCharCase noChange
+treeImage phylo/mouseStrains_18way.png