53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 lrnassar Fri Oct 2 13:52:36 2026 -0700 Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451 diff --git src/hg/makeDb/trackDb/human/gpnStar.ra src/hg/makeDb/trackDb/human/gpnStar.ra new file mode 100644 index 00000000000..429549a6b1d --- /dev/null +++ src/hg/makeDb/trackDb/human/gpnStar.ra @@ -0,0 +1,357 @@ +track gpnStarLogoM +shortLabel GPN-Star (M) Logo +longLabel GPN-Star (M, 447 mammals) sequence logo of predicted constraint +parent predictionScoresSuper +container multiWig +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig 0 2 +aggregate stacked +logo on +showSubtrackColorOnUi on +autoScale off +viewLimits 0:2 +viewLimitsMax 0:2 +maxHeightPixels 100:40:16 +visibility full + + track gpnStarLogoMA + shortLabel A + longLabel GPN-Star (M, 447 mammals) logo height of A + parent gpnStarLogoM + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/m447/A.bw + color 0,128,0 + priority 1 + + track gpnStarLogoMC + shortLabel C + longLabel GPN-Star (M, 447 mammals) logo height of C + parent gpnStarLogoM + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/m447/C.bw + color 0,0,255 + priority 2 + + track gpnStarLogoMG + shortLabel G + longLabel GPN-Star (M, 447 mammals) logo height of G + parent gpnStarLogoM + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/m447/G.bw + color 255,166,0 + priority 3 + + track gpnStarLogoMT + shortLabel T + longLabel GPN-Star (M, 447 mammals) logo height of T + parent gpnStarLogoM + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/m447/T.bw + color 255,0,0 + priority 4 + +track gpnStarLlrM +shortLabel GPN-Star (M) -LLR +longLabel GPN-Star (M, 447 mammals) -LLR per alternate allele +parent predictionScoresSuper +compositeTrack on +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig +autoScale off +alwaysZero on +viewLimits -3:10 +viewLimitsMax -16:16 +negateValues on +yLineOnOff on +yLineMark 0 +graphTypeDefault bar +maxHeightPixels 100:16:16 +windowingFunction mean+whiskers +visibility dense + + track gpnStarLlrMA + shortLabel Mutation: A + longLabel GPN-Star (M, 447 mammals) -LLR: Mutation is A + parent gpnStarLlrM on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/m447/llr_A.bw + color 140,60,60 + altColor 60,60,140 + priority 1 + + track gpnStarLlrMC + shortLabel Mutation: C + longLabel GPN-Star (M, 447 mammals) -LLR: Mutation is C + parent gpnStarLlrM on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/m447/llr_C.bw + color 140,60,60 + altColor 60,60,140 + priority 2 + + track gpnStarLlrMG + shortLabel Mutation: G + longLabel GPN-Star (M, 447 mammals) -LLR: Mutation is G + parent gpnStarLlrM on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/m447/llr_G.bw + color 140,60,60 + altColor 60,60,140 + priority 3 + + track gpnStarLlrMT + shortLabel Mutation: T + longLabel GPN-Star (M, 447 mammals) -LLR: Mutation is T + parent gpnStarLlrM on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/m447/llr_T.bw + color 140,60,60 + altColor 60,60,140 + priority 4 + +track gpnStarLogoV +shortLabel GPN-Star (V) Logo +longLabel GPN-Star (V, 100 vertebrates) sequence logo of predicted constraint +parent predictionScoresSuper +container multiWig +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig 0 2 +aggregate stacked +logo on +showSubtrackColorOnUi on +autoScale off +viewLimits 0:2 +viewLimitsMax 0:2 +maxHeightPixels 100:40:16 +visibility hide + + track gpnStarLogoVA + shortLabel A + longLabel GPN-Star (V, 100 vertebrates) logo height of A + parent gpnStarLogoV + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/v100/A.bw + color 0,128,0 + priority 1 + + track gpnStarLogoVC + shortLabel C + longLabel GPN-Star (V, 100 vertebrates) logo height of C + parent gpnStarLogoV + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/v100/C.bw + color 0,0,255 + priority 2 + + track gpnStarLogoVG + shortLabel G + longLabel GPN-Star (V, 100 vertebrates) logo height of G + parent gpnStarLogoV + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/v100/G.bw + color 255,166,0 + priority 3 + + track gpnStarLogoVT + shortLabel T + longLabel GPN-Star (V, 100 vertebrates) logo height of T + parent gpnStarLogoV + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/v100/T.bw + color 255,0,0 + priority 4 + +track gpnStarLlrV +shortLabel GPN-Star (V) -LLR +longLabel GPN-Star (V, 100 vertebrates) -LLR per alternate allele +parent predictionScoresSuper +compositeTrack on +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig +autoScale off +alwaysZero on +viewLimits -3:10 +viewLimitsMax -16:16 +negateValues on +yLineOnOff on +yLineMark 0 +graphTypeDefault bar +maxHeightPixels 100:16:16 +windowingFunction mean+whiskers +visibility hide + + track gpnStarLlrVA + shortLabel Mutation: A + longLabel GPN-Star (V, 100 vertebrates) -LLR: Mutation is A + parent gpnStarLlrV on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/v100/llr_A.bw + color 140,60,60 + altColor 60,60,140 + priority 1 + + track gpnStarLlrVC + shortLabel Mutation: C + longLabel GPN-Star (V, 100 vertebrates) -LLR: Mutation is C + parent gpnStarLlrV on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/v100/llr_C.bw + color 140,60,60 + altColor 60,60,140 + priority 2 + + track gpnStarLlrVG + shortLabel Mutation: G + longLabel GPN-Star (V, 100 vertebrates) -LLR: Mutation is G + parent gpnStarLlrV on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/v100/llr_G.bw + color 140,60,60 + altColor 60,60,140 + priority 3 + + track gpnStarLlrVT + shortLabel Mutation: T + longLabel GPN-Star (V, 100 vertebrates) -LLR: Mutation is T + parent gpnStarLlrV on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/v100/llr_T.bw + color 140,60,60 + altColor 60,60,140 + priority 4 + +track gpnStarLogoP +shortLabel GPN-Star (P) Logo +longLabel GPN-Star (P, 243 primates) sequence logo of predicted constraint +parent predictionScoresSuper +container multiWig +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig 0 2 +aggregate stacked +logo on +showSubtrackColorOnUi on +autoScale off +viewLimits 0:2 +viewLimitsMax 0:2 +maxHeightPixels 100:40:16 +visibility hide + + track gpnStarLogoPA + shortLabel A + longLabel GPN-Star (P, 243 primates) logo height of A + parent gpnStarLogoP + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/p243/A.bw + color 0,128,0 + priority 1 + + track gpnStarLogoPC + shortLabel C + longLabel GPN-Star (P, 243 primates) logo height of C + parent gpnStarLogoP + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/p243/C.bw + color 0,0,255 + priority 2 + + track gpnStarLogoPG + shortLabel G + longLabel GPN-Star (P, 243 primates) logo height of G + parent gpnStarLogoP + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/p243/G.bw + color 255,166,0 + priority 3 + + track gpnStarLogoPT + shortLabel T + longLabel GPN-Star (P, 243 primates) logo height of T + parent gpnStarLogoP + type bigWig 0 2 + bigDataUrl /gbdb/$D/gpnStar/p243/T.bw + color 255,0,0 + priority 4 + +track gpnStarLlrP +shortLabel GPN-Star (P) -LLR +longLabel GPN-Star (P, 243 primates) -LLR per alternate allele +parent predictionScoresSuper +compositeTrack on +html gpnStar +pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" +maxWindowToDraw 10000000 +mouseOverFunction noAverage +dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026) +type bigWig +autoScale off +alwaysZero on +viewLimits -3:10 +viewLimitsMax -16:16 +negateValues on +yLineOnOff on +yLineMark 0 +graphTypeDefault bar +maxHeightPixels 100:16:16 +windowingFunction mean+whiskers +visibility hide + + track gpnStarLlrPA + shortLabel Mutation: A + longLabel GPN-Star (P, 243 primates) -LLR: Mutation is A + parent gpnStarLlrP on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/p243/llr_A.bw + color 140,60,60 + altColor 60,60,140 + priority 1 + + track gpnStarLlrPC + shortLabel Mutation: C + longLabel GPN-Star (P, 243 primates) -LLR: Mutation is C + parent gpnStarLlrP on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/p243/llr_C.bw + color 140,60,60 + altColor 60,60,140 + priority 2 + + track gpnStarLlrPG + shortLabel Mutation: G + longLabel GPN-Star (P, 243 primates) -LLR: Mutation is G + parent gpnStarLlrP on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/p243/llr_G.bw + color 140,60,60 + altColor 60,60,140 + priority 3 + + track gpnStarLlrPT + shortLabel Mutation: T + longLabel GPN-Star (P, 243 primates) -LLR: Mutation is T + parent gpnStarLlrP on + type bigWig + bigDataUrl /gbdb/$D/gpnStar/p243/llr_T.bw + color 140,60,60 + altColor 60,60,140 + priority 4 +