@gmod/jbrowse

{ "formatVersion" : 1, "names" : { "type" : "Hash", "url" : "names/" }, "tracks" : [ { "chunkSize" : 20000, "key" : "DNA", "label" : "DNA", "type" : "SequenceTrack", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" }, { "autocomplete" : "all", "compress" : 0, "feature" : [ "remark" ], "key" : "Example Features", "label" : "ExampleFeatures", "style" : { "className" : "feature2" }, "track" : "ExampleFeatures", "type" : "FeatureTrack", "urlTemplate" : "tracks/ExampleFeatures/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "feature" : [ "protein_coding_primary_transcript", "polypeptide" ], "key" : "Name test track has a really long track label", "label" : "NameTest", "style" : { "className" : "feature2" }, "track" : "NameTest", "type" : "FeatureTrack", "urlTemplate" : "tracks/NameTest/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "feature" : [ "SNP" ], "key" : "Test SNPs", "label" : "snps", "style" : { "className" : "triangle hgred" }, "track" : "snps", "type" : "FeatureTrack", "urlTemplate" : "tracks/snps/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "description" : 1, "feature" : [ "polypeptide_domain" ], "key" : "Example motifs", "label" : "Motifs", "style" : { "className" : "feature3" }, "track" : "Motifs", "type" : "FeatureTrack", "urlTemplate" : "tracks/Motifs/{refseq}/trackData.json" }, { "autocomplete" : "all", "category" : "Alignments", "compress" : 0, "feature" : [ "match" ], "hooks" : { "modify" : "function( track, feature, div ) { div.style.height = (Math.random()*10+8)+'px'; div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()*5)];}" }, "key" : "Example alignments", "label" : "Alignments", "menuTemplate" : [ { "children" : [ { "children" : [ { "action" : "newWindow", "iconClass" : "dijitIconBookmark", "label" : "Query trin for {name}", "url" : "http://wiki.trin.org.au/{name}-{start}-{end}" }, { "iconClass" : "dijitIconSearch", "label" : "Query example.com for {name}", "url" : "http://example.com/{name}-{start}-{end}" } ], "label" : "Check gene on databases" }, { "label" : "2nd child of demo" }, { "label" : "3rd child: this is a track" } ], "label" : "Item with submenu" }, { "action" : "iframeDialog", "iconClass" : "dijitIconDatabase", "label" : "Open example.com in an iframe popup", "title" : "The magnificent example.com (feature {name})", "url" : "http://www.example.com?featurename={name}" }, { "action" : "xhrDialog", "iconClass" : "dijitIconDatabase", "label" : "Open popup with XHR HTML snippet (btw this is feature {name})", "title" : "function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }", "url" : "sample_data/test_snippet.html?featurename={name}:{start}-{end}" }, { "action" : "contentDialog", "content" : "function(track,feature,div) { return '<h2>'+feature.get('name')+'</h2><p>This is some test content!</p><p>This message brought to you by the number <span style=\"font-size: 300%\">'+Math.round(Math.random()*100)+'</span>.</p>';} ", "iconClass" : "dijitIconDatabase", "label" : "Popup with content snippet from a function (feature {name})", "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }" }, { "action" : "contentDialog", "content" : "<h2>{name}</h2><p>This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.</p>", "iconClass" : "dijitIconDatabase", "label" : "Popup with content snippet from string (feature {name})", "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }" }, { "action" : "function( evt ){ alert('Hi there! Ran the callback on feature '+this.feature.get('name')); }", "iconClass" : "dijitIconDatabase", "label" : "function(track,feature,div) { return 'Run a JS callback '+Math.random()+' title!'; }" } ], "style" : { "className" : "feature4" }, "track" : "Alignments", "type" : "FeatureTrack", "urlTemplate" : "tracks/Alignments/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "feature" : [ "gene" ], "key" : "Protein-coding genes", "label" : "Genes", "onClick" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}", "style" : { "className" : "feature5" }, "track" : "Genes", "type" : "FeatureTrack", "urlTemplate" : "tracks/Genes/{refseq}/trackData.json" }, { "autocomplete" : "all", "category" : "Genes", "compress" : 0, "feature" : [ "mRNA" ], "key" : "Frame usage", "label" : "ReadingFrame", "onClick" : { "label" : "search at NCBI", "url" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}" }, "style" : { "className" : "dblhelix" }, "track" : "ReadingFrame", "type" : "FeatureTrack", "urlTemplate" : "tracks/ReadingFrame/{refseq}/trackData.json" }, { "autocomplete" : "all", "category" : "Genes", "compress" : 0, "feature" : [ "CDS:predicted", "mRNA:exonerate", "mRNA:predicted" ], "key" : "Predicted genes", "label" : "CDS", "phase" : 1, "style" : { "className" : "cds", "linkTemplate" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}" }, "track" : "CDS", "type" : "FeatureTrack", "urlTemplate" : "tracks/CDS/{refseq}/trackData.json" }, { "autocomplete" : "all", "category" : "Genes", "compress" : 0, "description" : 1, "feature" : [ "mRNA:exonerate" ], "key" : "Exonerate predictions", "label" : "Transcript", "onClick" : "function() { alert('This is a user-configurable JavaScript action!'); };", "style" : { "arrowheadClass" : "transcript-arrowhead", "className" : "transcript", "subfeatureClasses" : { "CDS" : "transcript-CDS", "UTR" : "transcript-UTR" } }, "subfeatures" : true, "track" : "Transcript", "type" : "FeatureTrack", "urlTemplate" : "tracks/Transcript/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "description" : 1, "feature" : [ "BAC" ], "key" : "Fingerprinted BACs", "label" : "Clones", "style" : { "className" : "exon" }, "track" : "Clones", "type" : "FeatureTrack", "urlTemplate" : "tracks/Clones/{refseq}/trackData.json" }, { "autocomplete" : "all", "compress" : 0, "feature" : [ "EST_match:est" ], "key" : "ESTs", "label" : "EST", "style" : { "className" : "est" }, "track" : "EST", "type" : "FeatureTrack", "urlTemplate" : "tracks/EST/{refseq}/trackData.json" }, { "bicolor_pivot" : "mean", "key" : "BigWig Density - volvox_microarray", "label" : "volvox_microarray.bw_density", "storeClass" : "JBrowse/Store/BigWig", "type" : "JBrowse/View/Track/Wiggle/Density", "urlTemplate" : "../../raw/volvox/volvox_microarray.bw" }, { "key" : "BigWig XY - volvox_microarray", "label" : "volvox_microarray.bw_xyplot", "storeClass" : "JBrowse/Store/BigWig", "type" : "JBrowse/View/Track/Wiggle/XYPlot", "urlTemplate" : "../../raw/volvox/volvox_microarray.bw", "variance_band" : "true" }, { "bicolor_pivot" : "mean", "key" : "BigWig Density - volvox_sine", "label" : "volvox_sine_density", "storeClass" : "JBrowse/Store/BigWig", "type" : "JBrowse/View/Track/Wiggle/Density", "urlTemplate" : "../../raw/volvox/volvox_sine.bw" }, { "key" : "BigWig XY - volvox_sine", "label" : "volvox_sine_xyplot", "storeClass" : "JBrowse/Store/BigWig", "style" : { "bg_color" : "#ccc" }, "type" : "JBrowse/View/Track/Wiggle/XYPlot", "urlTemplate" : "../../raw/volvox/volvox_sine.bw" }, { "key" : "volvox-sorted.bam", "label" : "volvox-sorted.bam", "storeClass" : "JBrowse/Store/SeqFeature/BAM", "style" : { "arrowheadClass" : "arrowhead", "className" : "alignment", "labelScale" : 100 }, "type" : "JBrowse/View/Track/Alignments", "urlTemplate" : "../../raw/volvox/volvox-sorted.bam" }, { "key" : "volvox-sorted Coverage", "label" : "volvox-sorted.bam_coverage", "max_score" : 35, "min_score" : 0, "storeClass" : "JBrowse/Store/SeqFeature/BAM", "type" : "JBrowse/View/Track/FeatureCoverage", "urlTemplate" : "../../raw/volvox/volvox-sorted.bam" }, { "compress" : 0, "key" : "volvox_microarray.wig", "label" : "volvox_microarray.wig", "style" : { "className" : "image" }, "type" : "ImageTrack.Wiggle", "urlTemplate" : "tracks/volvox_microarray.wig/{refseq}/trackData.json" }, { "compress" : 0, "key" : "Simulated next-gen reads", "label" : "bam_simulated", "style" : { "className" : "basic", "featureCss" : "background-color: #66F; height: 8px", "histCss" : "background-color: #88F", "histScale" : 2 }, "type" : "FeatureTrack", "urlTemplate" : "tracks/bam_simulated/{refseq}/trackData.json" }, { "category" : "Miscellaneous", "key" : "GFF3Tabix - volvox.gff3 in-memory adaptor", "label" : "volvox_gff3_tabix", "maxFeatureScreenDensity" : 0.05, "metadata" : { "description" : "This is just all the features in the volvox.gff3 test file, displayed using GFF3 and tabix" }, "storeClass" : "JBrowse/Store/SeqFeature/GFF3Tabix", "tbiUrlTemplate" : "volvox.sort.gff3.gz.tbi", "type" : "CanvasFeatures", "urlTemplate" : "volvox.sort.gff3.gz.1" } ] }