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biodall.html
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<script language="javascript" src="//www.biodalliance.org/release-0.13/dalliance-compiled.js"></script>
<script language="javascript">
new Browser({
chr: '7',
viewStart: 87057510,
viewEnd: 87126847,
cookieKey: 'WESTARC_human-grc_h37-fp',
coordSystem: {
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: '37',
ucscName: 'hg19'
},
sources: [{name: 'Genome',
twoBitURI: '//www.biodalliance.org/datasets/hg19.2bit',
tier_type: 'sequence',
provides_entrypoints: true,
pinned: true
},
{name: 'Genes',
desc: 'Gene structures from GENCODE 19',
bwgURI: '//www.biodalliance.org/datasets/gencode.bb',
stylesheet_uri: '//www.biodalliance.org/stylesheets/gencode.xml',
collapseSuperGroups: true,
trixURI: '//www.biodalliance.org/datasets/geneIndex.ix'},
{name: 'SNPs',
tier_type: 'ensembl',
species:'human',
type: 'variation',
disabled: true,
featureInfoPlugin: function(f, info) {
if (f.id) {
info.add('SNP', makeElement('a', f.id, {href: 'http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=' + f.id, target: '_newtab'}));
}
}
},
{name: "HG00103_BAM",
bamURI: "https://43.240.99.48/exome-data/HG00103.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam"},
{name: "HG00108_BAM",
bamURI: "https://43.240.99.48/exome-data/HG00108.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam"},
{name: "HG00259_BAM",
bamURI: "https://43.240.99.48/exome-data/HG00259.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam"},
{name: "HG00284_BAM",
bamURI: "https://43.240.99.48/exome-data/HG00284.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam"},
{name: 'Repeats',
desc: 'Repeat annotation from Ensembl',
disabled: true,
bwgURI: '//www.biodalliance.org/datasets/repeats.bb',
stylesheet_uri: '//www.biodalliance.org/stylesheets/bb-repeats.xml'},
{name: 'Conservation',
desc: 'Conservation',
disabled: true,
bwgURI: '//www.biodalliance.org/datasets/phastCons46way.bw',
noDownsample: true},
{name:"GWAS Catalog",
desc:"NHGRI GWAS Catalog",
disabled: true,
style:[{type:"default",style:{glyph:"PLIMSOLL",SIZE:"12",STROKECOLOR:"black",FGCOLOR:"red",BUMP:"yes"}}],forceReduction:-1,bwgURI:"http://ngs.sanger.ac.uk/production/uk10k/dalliance/gwascatalog.bb"},
{name: 'CpG',
desc: 'CpG observed/expected ratio',
disabled: true,
uri: 'http://www.derkholm.net:8080/das/hg19comp/',
// stylesheet_uri: 'http://www.derkholm.net/dalliance-test/stylesheets/cpg.xml'
quantLeapThreshold: 0.8,
forceReduction: -1,
style: [{type: 'cpgoe',
style: {glyph: 'LINEPLOT',
FGCOLOR: 'blue', HEIGHT: '50', MIN: 0, MAX: 1.2}}]
},
{name: 'GM12878 ChromHMM',
disabled: true,
desc: 'GM12878 ChromHMM Genome Segmentation',
pennant: '//genome.ucsc.edu/images/encodeThumbnail.jpg',
bwgURI: '//www.biodalliance.org/datasets/encode/gm12878.ChromHMM.bb',
style: [{type: 'bigbed', style: {glyph: 'BOX', FGCOLOR: 'black', BGCOLOR: 'blue', HEIGHT: 8, BUMP: false, LABEL: false, ZINDEX: 20, BGITEM: true, id: 'style1'}}, {type: 'bb-translation', style: {glyph: 'BOX', FGCOLOR: 'black', BGITEM: true, BGCOLOR: 'red', HEIGHT: 10, BUMP: true, ZINDEX: 20, id: 'style2'}}, {type: 'bb-transcript', style: {glyph: 'BOX', FGCOLOR: 'black', BGCOLOR: 'white', HEIGHT: 10, ZINDEX: 10, BUMP: true, LABEL: true, id: 'style3'}}]}
],
fullScreen: true,
browserLinks: {
Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr${chr}:${start}-${end}',
Sequence: 'http://www.derkholm.net:8080/das/hg19comp/sequence?segment=${chr}:${start},${end}'
},
hubs: ['http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt', {url: 'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt', genome: 'hg19', mapping: 'hg19ToHg38'}],
});
</script>
<div id="svgHolder"></div>