URL parameter specification (effective v13)
Thursday, December 27, 2012
Last updated: 11/20/2013
To tell which genome assembly to use
parameter namegenome valueone of hg19, mm9, dm3, tair10, danRer7, spombe201203, AGPv2 examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19 notewhen this parameter is used alone, it will load up a blank Browser (with no tracks displayed)
this parameter must be used along with all the rest of the parameters
To retrieve a saved session
parameter namesession valuethe session ID examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&session=your_session_here noteby using this parameter all the following parameters will be neglected
To show data over a specific genomic location
parameter namecoordinate valuecoordinate must be in form of "chr1:123-456" examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&coordinate=chr7:26663835-28123541 notethis parameter cannot be used when parameter "geneset" is present
To show data over a gene set (or set of genomic intervals)
parameter namegeneset valuea list of gene symbols, or coordinates, all joined by comma examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&geneset=chr7:26675831-28111542,chr7:101818721-102732764,cyp2c19 notethis parameter cannot be used when parameter "coordinate" is present
To run genomic juxtaposition on a BED track
parameter namejuxtapose valueif the bed track is native, use internal track name (e.g. "refGene")
else if it is custom bed track, use track URL, a second parameter "juxtaposecustom=on" must also be supplied examplenative: http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=refGene
To display a tabular datahub (deprecated)
parameter namedatahub valueURL of the hub descriptor file examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub=http://vizhub.wustl.edu/hubSample/hg19/hub2.txt noteonly one hub URL can be used
To display a JSON datahub
parameter namedatahub_jsonfile valueURL to the JSON file examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://vizhub.wustl.edu/hubSample/hg19/hub.json noteonly one hub URL can be used
Refer to this post about how to prepare your JSON datahub.
To add native heatmap tracks (bedgraph/bigwig/categorical)
parameter namehmtk valuetrack names joined by comma examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&hmtk=GSM469970,GSM521901,GSM521895,GSM521897,GSM469974,GSM521913,GSM469968,GSM521889,GSM945297_2,GSM608165_1,GSM733692_1,GSM788085_1,GSM733776_1,GSM607494_1,GSM945228_2,GSM945228_1 noteuse internal track name, but not the label printed on the left of track image in the browser
To add native genomic annotation tracks
parameter namegftk valuetrackname1,mode1,trackname2,mode2,... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=refGene,full,gc5Base,show notecurrently, native long-range genome interaction tracks are also declared with this parameter
the mode can never be "hide"
if the track is quantitative, the mode can only be "show",
if the track is positional (bed), the mode can be "thin", "full", "density"
if the track is long-range interaction, mode can be "arc", "trihm", "thin", "full", or "density"
To add native metadata term
parameter namemetadata valuemetadata terms joined by comma, space in term names must be coded as %20 examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&metadata=Histone%20Mark,12003 notenone-leaf terms are shown as "words"
leaf terms must be used as internal ID
If you want to create custom metadata terms, use JSON datahub
To add custom bedGraph track
parameter namecustombedgraph valuename1,url1,name2,url2,... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&custombedgraph=track%20No.1,http://vizhub.wustl.edu/hubSample/hg19/qual1.gz,track%20No.2,http://vizhub.wustl.edu/hubSample/hg19/qual2.gz notespecial characters in the names must be escaped
To add custom bigWig track
parameter namecustombigwig valuename1,url1,name2,url2,... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&custombigwig=track%20No.1,http://vizhub.wustl.edu/hubSample/hg19/sample.bigWig,track%20No.2,http://vizhub.wustl.edu/hubSample/hg19/GSM429321.bigWig notespecial characters in the names must be escaped
To add custom bed track (positional annotations)
parameter namecustombed valuename1,url1,mode1,name2,url2,mode2,... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&custombed=bedTrack%20No.1,http://vizhub.wustl.edu/hubSample/hg19/bed.gz,full,bedTrack%20No.2,http://vizhub.wustl.edu/hubSample/hg19/mer41b.gz,full notemode must be one of "thin", "full", "density"
special characters in the names must be escaped
To add custom long-range interaction track
parameter namecustomlongrange valuename1,url1,mode1,name2,url2,mode2,.... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&customlongrange=trackname,http://vizhub.wustl.edu/hubSample/hg19/K562POL2.gz,arc notemode can be one of "arc", "trihm", "thin", "full", "density"
special characters in the names must be escaped
To add custom read-alignment (BAM) track
parameter namecustombam valuename1,url1,mode1,name2,url2,mode2,... examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&custombam=tempest,http://vizhub.wustl.edu/hubSample/hg19/bam1.bam,density notemode can be one of "thin", "full", "density"
special characters in the names must be escaped
To show secondary panel (experimental)
parameter namesplinters valuecoordinate (e.g. chr5:5000000-5100000) examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gc5Base,show&splinters=chr5:5000000-5100000 notemultiple coordinates can be added, join them by comma. Only use this if your screen is wide enough...
To show default tracks and contents for a genome assembly
parameter namedefaultContent valuestring "on" examplehttp://epigenomegateway.wustl.edu/browser/?genome=hg18&defaultContent=on note
