diff --git a/frontend/src/model/genomes/hg19/annotationTracks.json b/frontend/src/model/genomes/hg19/annotationTracks.json index 271c200d..46bcd43b 100644 --- a/frontend/src/model/genomes/hg19/annotationTracks.json +++ b/frontend/src/model/genomes/hg19/annotationTracks.json @@ -1,416 +1,452 @@ { - "Ruler": [ - { - "type": "ruler", - "label": "Ruler", - "name": "Ruler" - } - ], - "Genes": [ - { - "name": "refGene", - "label": "RefSeq genes", - "filetype": "geneAnnotation" - }, - - { - "name": "gencodeV29", - "label": "GENCODE V29 genes", - "options": { - "categoryColors": { - "coding": "rgb(0,60,179)", - "nonCoding": "rgb(0,128,0)", - "pseudogene": "rgb(230,0,172)", - "problem": "rgb(255,0,0)", - "polyA": "rgb(0,0,51)" - } - }, - "filetype": "geneAnnotation" - }, - { - "name": "gencodeV29Basic", - "label": "GENCODE V29 basic genes", - "options": { - "categoryColors": { - "coding": "rgb(0,60,179)", - "nonCoding": "rgb(0,128,0)", - "pseudogene": "rgb(230,0,172)", - "problem": "rgb(255,0,0)", - "polyA": "rgb(0,0,51)" + "Ruler": [ + { + "type": "ruler", + "label": "Ruler", + "name": "Ruler" + } + ], + "Genes": [ + { + "name": "refGene", + "label": "RefSeq genes", + "filetype": "geneAnnotation" + }, + + { + "name": "gencodeV29", + "label": "GENCODE V29 genes", + "options": { + "categoryColors": { + "coding": "rgb(0,60,179)", + "nonCoding": "rgb(0,128,0)", + "pseudogene": "rgb(230,0,172)", + "problem": "rgb(255,0,0)", + "polyA": "rgb(0,0,51)" + } + }, + "filetype": "geneAnnotation" + }, + { + "name": "gencodeV29Basic", + "label": "GENCODE V29 basic genes", + "options": { + "categoryColors": { + "coding": "rgb(0,60,179)", + "nonCoding": "rgb(0,128,0)", + "pseudogene": "rgb(230,0,172)", + "problem": "rgb(255,0,0)", + "polyA": "rgb(0,0,51)" + } + }, + "filetype": "geneAnnotation" + }, + { + "name": "gencodeV19", + "label": "GENCODE V19 genes", + "url": "https://vizhub.wustl.edu/public/hg19/gencodeV19.refBed.gz", + "options": { + "categoryColors": { + "coding": "rgb(0,60,179)", + "nonCoding": "rgb(0,128,0)", + "pseudogene": "rgb(230,0,172)", + "problem": "rgb(255,0,0)", + "polyA": "rgb(0,0,51)" + } + }, + "filetype": "refbed" + } + ], + "Variation": [ + { + "name": "Snp", + "label": "Snps from Ensembl", + "type": "snp" + } + ], + "RepeatMasker": { + "All Repeats": [ + { + "name": "rmsk_all", + "label": "RepeatMasker", + "filetype": "repeatmasker", + "url": "https://vizhub.wustl.edu/public/hg19/rmsk16.bb", + "height": 40 + } + ] + }, + "Conservation": [ + { + "name": "vertebratephastCons46way", + "label": "Vertebrate PhastCons 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/vertebratephastCons46way.gz", + "height": 50, + "options": { "color": "#006385"} + }, + { + "name": "primatephastCons46way", + "label": "Primate PhastCons 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/primatephastCons46way.gz", + "height": 50, + "options": { "color": "#006385"} + }, + { + "name": "placentalphastCons46way", + "label": "Placental PhastCons 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/placentalphastCons46way.gz", + "height": 50, + "options": { "color": "#006385"} + }, + { + "name": "vertebratephyloP46way", + "label": "Vertebrate PhyloP 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/vertebratephyloP46way.gz", + "height": 50, + "options": { "color": "#006385", "color2": "#852100"} + }, + { + "name": "primatephyloP46way", + "label": "Primate PhyloP 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/primatephyloP46way.gz", + "height": 50, + "options": { "color": "#006385", "color2": "#852100"} + }, + { + "name": "placentalphyloP46way", + "label": "Placental PhyloP 46-way", + "filetype": "bedgraph", + "url": "https://egg.wustl.edu/d/hg19/placentalphyloP46way.gz", + "height": 50, + "options": { "color": "#006385", "color2": "#852100"} + } + ], + "Genome Annotation": [ + { + "name": "blacklist", + "label": "hg19 Encode Blacklist", + "filetype": "bed", + "url": "https://epgg-test.wustl.edu/d/hg19/hg19.blacklist.bed.gz", + "height": 21, + "options": { + "color": "#000000" + }, + "details": { + "source": "mod/mouse/humanENCODE Blacklists", + "download url": "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg19-human/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz" + } + }, + { + "type": "categorical", + "name": "CpG Context", + "url": "https://epgg-test.wustl.edu/d/hg19/hg19_cpgIslands_Shores_Shelves.bed.gz", + "height": 30, + "options": { + "label": "CpG Context", + "category": { + "Island": {"name": "Island", "color": "#05B678"}, + "Shore": { "name": "Shore", "color": "#F5DC69"}, + "Shelf": { "name": "Shelf", "color": "#07C6EC"} + }, + "backgroundColor":"#071CEC" + } + }, + { + "type": "categorical", + "name": "CpG Context (unmasked)", + "url": "https://epgg-test.wustl.edu/d/hg19/hg19_cpgIslands_unmasked_Shores_Shelves.bed.gz", + "height": 30, + "options": { + "label": "CpG Context (unmasked)", + "category": { + "Island": {"name": "Island", "color": "#05B678"}, + "Shore": { "name": "Shore", "color": "#F5DC69"}, + "Shelf": { "name": "Shelf", "color": "#07C6EC"} + }, + "backgroundColor":"#071CEC" + } + }, + { + "type": "categorical", + "name": "CpG Islands", + "url": "https://epgg-test.wustl.edu/d/hg19/hg19_cpgIslands_category.bed.gz", + "height": 30, + "options": { + "label": "CpG Context", + "category": { + "CGI": {"name": "CGI", "color": "#FE8801"} } - }, - "filetype": "geneAnnotation" - }, - { - "name": "gencodeV19", - "label": "GENCODE V19 genes", - "url": "https://vizhub.wustl.edu/public/hg19/gencodeV19.refBed.gz", - "options": { - "categoryColors": { - "coding": "rgb(0,60,179)", - "nonCoding": "rgb(0,128,0)", - "pseudogene": "rgb(230,0,172)", - "problem": "rgb(255,0,0)", - "polyA": "rgb(0,0,51)" + } + }, + { + "type": "categorical", + "name": "CpG Islands (unmasked)", + "url": 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], - "Genome Annotation": [ - { - "name": "blacklist", - "label": "hg19 Encode Blacklist", - "filetype": "bed", - "url": "https://epgg-test.wustl.edu/d/hg19/hg19.blacklist.bed.gz", - "height": 21, - "options": { - "color": "#000000" - }, - "details": { - "source": "mod/mouse/humanENCODE Blacklists", - "download url": "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg19-human/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz" - } - }, - { - "type": "categorical", - "name": "CpG Context", - "url": "https://epgg-test.wustl.edu/d/hg19/hg19_cpgIslands_Shores_Shelves.bed.gz", - "height": 30, - "options": { - "label": "CpG Context", - "category": { - "Island": {"name": "Island", "color": "#05B678"}, - "Shore": { "name": "Shore", "color": "#F5DC69"}, - "Shelf": { "name": "Shelf", "color": "#07C6EC"} + } + }, + { + "name": "CpGs", + "label": "CpGs", + "filetype": "bed", + "url": "https://egg.wustl.edu/d/hg19/CpGsites.gz", + "height": 21, + "options": { + "color": "#cc00cc" + } + 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ENCODE/CRG(Guigo)", - "filetype": "bigwig", - "url": "https://egg.wustl.edu/d/hg19/wgEncodeCrgMapabilityAlign75mer.bigWig", - "height": 30, - "options": { - "yScale": "fixed", - "yMin": 0, - "yMax": 1 - }, - "details": { - "datafiletype": "Mapability", - "subId": 4945, - "size": "75mer", - "uniqueness": "no more than 2 mismatches", - "software": "GEM", - "download": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/" - } - }, - { - "name": "wgEncodeCrgMapabilityAlign50mer", - "label": "50mer alignability ENCODE/CRG(Guigo)", - "filetype": "bigwig", - "url": "https://egg.wustl.edu/d/hg19/wgEncodeCrgMapabilityAlign50mer.bigWig", - "height": 50, - "options": { - "yScale": "fixed", - "yMin": 0, - "yMax": 1 - }, - "details": { - "datafiletype": "Mapability", - "subId": 4945, - "size": "50mer", - "uniqueness": "no more than 2 mismatches", - "software": "GEM", - "download": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/" - } - }, - { - "name": "wgEncodeCrgMapabilityAlign40mer", - "label": "40mer alignability ENCODE/CRG(Guigo)", - "filetype": "bigwig", - "url": "https://egg.wustl.edu/d/hg19/wgEncodeCrgMapabilityAlign40mer.bigWig", - "height": 30, - "options": { - "yScale": "fixed", - "yMin": 0, - "yMax": 1 - }, - "details": { - "datafiletype": "Mapability", - "subId": 4945, - "size": "40mer", - "uniqueness": "no more than 2 mismatches", - "software": "GEM", - "download": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/" - } - }, - { - "name": "wgEncodeCrgMapabilityAlign36mer", - "label": "36mer alignability ENCODE/CRG(Guigo)", - "filetype": "bigwig", - "url": "https://egg.wustl.edu/d/hg19/wgEncodeCrgMapabilityAlign36mer.bigWig", - "height": 30, - "options": { - "yScale": "fixed", - "yMin": 0, - "yMax": 1 - }, - "details": { - "datafiletype": "Mapability", - "subId": 4945, - "size": "36mer", - "uniqueness": "no more than 2 mismatches", - "software": "GEM", - "download": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/" - } - }, - { - "name": "wgEncodeCrgMapabilityAlign24mer", - "label": "24mer alignability ENCODE/CRG(Guigo)", - "filetype": "bigwig", - "url": "https://egg.wustl.edu/d/hg19/wgEncodeCrgMapabilityAlign24mer.bigWig", - "height": 30, - "options": { - "yScale": "fixed", - "yMin": 0, - "yMax": 1 - }, - "details": { - "datafiletype": "Mapability", - "subId": 4945, - "size": "24mer", - "uniqueness": "no more than 2 mismatches", - "software": "GEM", - "download": "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/" - } - } - ] -} + } + ] + } + \ No newline at end of file