Updates

Author: cmdcolin

genark2jbrowse/taxon_images/283036.json

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+{
+  "imageUrl": "https://upload.wikimedia.org/wikipedia/commons/thumb/4/41/Walleye_%28Sander_vitreus%29_%281%29.jpg/500px-Walleye_%28Sander_vitreus%29_%281%29.jpg",
+  "pageUrl": "https://wikipedia.org/wiki/Sander vitreus"
+}

hubs/GCF/031/162/955/GCF_031162955.1/config.json

@@ -0,0 +1,268 @@
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+email genome-www@soe.ucsc.edu
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+
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+groups groups.txt
+description walleye (19-12246 2023)
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+organism sanVit1 Sep. 2023
+defaultPos NC_135855.1:13747230-13757230
+scientificName Sander vitreus
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+
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+urlLabel NCBI Nucleotide database:
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+
+track cytoBandIdeo
+shortLabel Chromosome Band (Ideogram)
+longLabel Ideogram for Orientation
+group map
+visibility dense
+type bigBed 4 +
+bigDataUrl bbi/GCF_031162955.1_sanVit1.cytoBand.bb
+
+track gc5Base
+shortLabel GC Percent
+longLabel GC Percent in 5-Base Windows
+group map
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+autoScale Off
+maxHeightPixels 128:36:16
+graphTypeDefault Bar
+gridDefault OFF
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+viewLimits 30:70
+type bigWig 0 100
+bigDataUrl bbi/GCF_031162955.1_sanVit1.gc5Base.bw
+html html/GCF_031162955.1_sanVit1.gc5Base
+
+track tanDups
+shortLabel Tandem Dups
+longLabel Paired identical sequences
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+visibility hide
+type bigBed 12
+group map
+html html/GCF_031162955.1_sanVit1.tanDups
+
+    track tandemDups
+    parent tanDups on
+    shortLabel Tandem Dups
+    longLabel Paired exactly identical sequence survey over entire genome assembly
+    bigDataUrl bbi/GCF_031162955.1_sanVit1.tandemDups.bb
+    type bigBed 12
+
+track repeatMasker
+shortLabel RepeatMasker
+longLabel RepeatMasker Repetitive Elements
+type bigRmsk 9 +
+visibility pack
+group varRep
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+maxWindowToDraw 5000000
+html html/GCF_031162955.1_sanVit1.repeatMasker
+
+track simpleRepeat
+shortLabel Simple Repeats
+longLabel Simple Tandem Repeats by TRF
+group varRep
+visibility dense
+type bigBed 4 +
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+html html/GCF_031162955.1_sanVit1.simpleRepeat
+
+track refSeqComposite
+compositeTrack on
+shortLabel NCBI RefSeq
+longLabel RefSeq gene predictions from NCBI
+group genes
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+type bigBed
+dragAndDrop subTracks
+allButtonPair on
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+html html/GCF_031162955.1_sanVit1.refSeqComposite
+priority 2
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+        parent refSeqComposite on
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+        shortLabel RefSeq All
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+        idXref ncbiRefSeqLink mrnaAcc name
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+        color 12,12,120
+        parent refSeqComposite on
+        shortLabel RefSeq Curated
+        longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
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+        shortLabel RefSeq Predicted
+        longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
+        type bigGenePred
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+        shortLabel RefSeq Other
+        longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
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+
+        track ncbiRefSeqPsl
+        priority 5
+        parent refSeqComposite off
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+        longLabel RefSeq Alignments of RNAs
+        type bigPsl
+        searchIndex name
+        bigDataUrl bbi/GCF_031162955.1_sanVit1.bigPsl.bb
+        indelDoubleInsert on
+        indelQueryInsert on
+        showDiffBasesAllScales .
+        showDiffBasesMaxZoom 10000.0
+        showCdsMaxZoom 10000.0
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+        pslSequence no
+        baseColorUseSequence lfExtra
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+        color 0,0,0
+
+track cpgIslands
+compositeTrack on
+shortLabel CpG Islands
+longLabel CpG Islands (Islands < 300 Bases are Light Green)
+group regulation
+visibility dense
+type bigBed 4 +
+html html/GCF_031162955.1_sanVit1.cpgIslands
+
+    track cpgIslandExt
+    parent cpgIslands off
+    shortLabel CpG Islands
+    longLabel CpG Islands (Islands < 300 Bases are Light Green)
+    type bigBed 4 +
+    priority 1
+    bigDataUrl bbi/GCF_031162955.1_sanVit1.cpgIslandExt.bb
+
+    track cpgIslandExtUnmasked
+    parent cpgIslands on
+    shortLabel Unmasked CpG
+    longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
+    type bigBed 4 +
+    priority 2
+    bigDataUrl bbi/GCF_031162955.1_sanVit1.cpgIslandExtUnmasked.bb
+
+track windowMasker
+shortLabel WM + SDust
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+group varRep
+visibility dense
+type bigBed 3
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+html html/GCF_031162955.1_sanVit1.windowMasker
+
+track allGaps
+shortLabel All Gaps
+longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
+group map
+visibility hide
+type bigBed 3
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+html html/GCF_031162955.1_sanVit1.allGaps
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+track augustus
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+visibility dense
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+html html/GCF_031162955.1_sanVit1.augustus
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+track xenoRefGene
+shortLabel RefSeq mRNAs
+longLabel RefSeq mRNAs mapped to this assembly
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hubs/GCF/031/162/955/GCF_031162955.1/hub.txt

@@ -0,0 +1,4 @@
+{
+  "imageUrl": "https://upload.wikimedia.org/wikipedia/commons/thumb/4/41/Walleye_%28Sander_vitreus%29_%281%29.jpg/500px-Walleye_%28Sander_vitreus%29_%281%29.jpg",
+  "pageUrl": "https://wikipedia.org/wiki/Sander vitreus"
+}

hubs/GCF/031/162/955/GCF_031162955.1/image.json

@@ -0,0 +1,11 @@
+{
+  "accession": "GCF_031162955.1",
+  "assembly": "GCF_031162955.1_sanVit1",
+  "scientificName": "Sander vitreus",
+  "commonName": "walleye (19-12246 2023)",
+  "taxonId": 283036,
+  "identical": false,
+  "genBank": "GCA_031162955.1",
+  "refSeq": "GCF_031162955.1",
+  "hubFileLocation": "https://hgdownload.soe.ucsc.edu/hubs/GCF/031/162/955/GCF_031162955.1/hub.txt"
+}