1b34ddd99f21b5b31c9c0b65ed7957fe29d29fb9
markd
  Tue Aug 19 10:21:11 2025 -0700
updates to recount3 tracks (not complete)

diff --git src/hg/makeDb/trackDb/human/hg38/recount3.ra src/hg/makeDb/trackDb/human/hg38/recount3.ra
index dbe148e3399..12387295377 100644
--- src/hg/makeDb/trackDb/human/hg38/recount3.ra
+++ src/hg/makeDb/trackDb/human/hg38/recount3.ra
@@ -1,119 +1,117 @@
 
 
 # Note: sjPair filter at the parent doesn't work,
 # it was always reset to the default.  So they
 # we move to only being on the individual tracks.
 
 track recount3
 shortLabel recount3
 longLabel recount 3 introns
 group rna
 type bigBed 9 +
 visibility hide
-spectrum on
-scoreMax 225
 html recount3
 compositeTrack on
 noParentConfig on
 
-    track gtex
+    track recount3_gtex
     showCfg on
     shortLabel GTEX
     longLabel recount 3 GTEX introns
     bigDataUrl /gbdb/$D/recount3/gtexv2.bb
     labelFields none
     mouseOver $readcount supporting split reads<br>Strand $strand<br>Size $size<br>Splice donor $donor<br>Splice acceptor $acceptor
     iframeUrl https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation=gtexv2&jid=$$&coords=$S:${-$}
     iframeOptions height='300' width='1000' scrolling='yes'
-    decorator.default.bigDataUrl /gbdb/$D/recount3/decgtexv2.bb
     parent recount3
     priority 1
+    itemRgb on
     filterLabel.strand Strand
     filterType.strand multiple
     filterValues.strand +,-,.
     filterLabel.readcount Filter by supporting split reads
     filterByRange.readcount on
     filter.readcount 10000:2000000000
     filterLimits.readcount 0:2000000000
     filterLabel.size Filter by intron size
     filterByRange.size on
     filter.size 30:100000
     filterLabel.sjPair Filter by splice junctions (format GT/AG)
     filterType.sjPair wildcard
     filterText.sjPair *
 
-    track tcga
+    track recount3_tcga
     shortLabel TCGA
     longLabel recount 3 TCGA introns
     bigDataUrl /gbdb/$D/recount3/tcgav2.bb
     labelFields none
     mouseOver $readcount supporting split reads<br>Strand $strand<br>Size $size<br>Splice donor $donor<br>Splice acceptor $acceptor
     iframeUrl https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation=tcgav2&jid=$$&coords=$S:${-$}
     iframeOptions height='300' width='1000' scrolling='yes'
-    decorator.default.bigDataUrl /gbdb/$D/recount3/dectcgav2.bb
     parent recount3
     priority 2
+    itemRgb on
     filterLabel.strand Strand
     filterType.strand multiple
     filterValues.strand +,-,.
     filterLabel.readcount Filter by supporting split reads
     filterByRange.readcount on
     filter.readcount 10000:2000000000
     filterLimits.readcount 0:2000000000
     filterLabel.size Filter by intron size
     filterByRange.size on
     filter.size 30:100000
     filterLabel.sjPair Filter by splice junctions (format GT/AG)
     filterType.sjPair wildcard
     filterText.sjPair *
 
-    track srav3h
+    track recount3_srav3h
     shortLabel SRA
     longLabel recount 3 SRA introns
     bigDataUrl /gbdb/$D/recount3/srav3h.bb
     labelFields none
     maxWindowToDraw 10000000
     mouseOver $readcount supporting split reads<br>Strand $strand<br>Size $size<br>Splice donor $donor<br>Splice acceptor $acceptor
     iframeUrl https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation=srav3h&jid=$$&coords=$S:${-$}
     iframeOptions height='300' width='1000' scrolling='yes'
-    decorator.default.bigDataUrl /gbdb/$D/recount3/decsrav3h.bb
     parent recount3
     priority 3
+    itemRgb on
     filterLabel.strand Strand
     filterType.strand multiple
     filterValues.strand +,-,.
     filterLabel.readcount Filter by supporting split reads
     filterByRange.readcount on
     filter.readcount 10000:2000000000
     filterLimits.readcount 0:2000000000
     filterLabel.size Filter by intron size
     filterByRange.size on
     filter.size 30:100000
     filterLabel.sjPair Filter by splice junctions (format GT/AG)
     filterType.sjPair wildcard
     filterText.sjPair *
 
-    track ccle
+    track recount3_ccle
     shortLabel CCLE
     longLabel recount 3 CCLE introns
     bigDataUrl /gbdb/$D/recount3/ccle.bb
     labelFields none
     mouseOver $readcount supporting split reads<br>Strand $strand<br>Size $size<br>Splice donor $donor<br>Splice acceptor $acceptor
     iframeUrl https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation=ccle&jid=$$&coords=$S:${-$}
     iframeOptions height='300' width='1000' scrolling='yes'
-    decorator.default.bigDataUrl /gbdb/$D/recount3/decccle.bb
     parent recount3
     priority 4
+    itemRgb on
     filterLabel.strand Strand
     filterType.strand multiple
     filterValues.strand +,-,.
     filterLabel.readcount Filter by supporting split reads
     filterByRange.readcount on
     filter.readcount 10000:2000000000
     filterLimits.readcount 0:2000000000
     filterLabel.size Filter by intron size
     filterByRange.size on
     filter.size 30:100000
     filterLabel.sjPair Filter by splice junctions (format GT/AG)
     filterType.sjPair wildcard
     filterText.sjPair *