URL parameter specification (effective v13)

Last updated: 11/20/2013

To tell which genome assembly to use

parameter name	genome
value	one of hg19, mm9, dm3, tair10, danRer7, spombe201203, AGPv2
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19
note	when 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 name	session
value	the session ID
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&session=your_session_here
note	by using this parameter all the following parameters will be neglected

To show data over a specific genomic location

parameter name	coordinate
value	coordinate must be in form of "chr1:123-456"
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&coordinate=chr7:26663835-28123541
note	this parameter cannot be used when parameter "geneset" is present

To show data over a gene set (or set of genomic intervals)

parameter name	geneset
value	a list of gene symbols, or coordinates, all joined by comma
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&geneset=chr7:26675831-28111542,chr7:101818721-102732764,cyp2c19
note	this parameter cannot be used when parameter "coordinate" is present

To run genomic juxtaposition on a BED track

parameter name	juxtapose
value	if 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
example	native: http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=refGene custom: http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=http://vizhub.wustl.edu/hubSample/hg19/bed.gz&juxtaposecustom=on
note

To display a tabular datahub (deprecated)

parameter name	datahub
value	URL of the hub descriptor file
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub=http://vizhub.wustl.edu/hubSample/hg19/hub2.txt
note	only one hub URL can be used

To display a JSON datahub

parameter name	datahub_jsonfile
value	URL to the JSON file
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://vizhub.wustl.edu/hubSample/hg19/hub.json
note	only 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 name	hmtk
value	track names joined by comma
example	http://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
note	use internal track name, but not the label printed on the left of track image in the browser

To add native genomic annotation tracks

parameter name	gftk
value	trackname1,mode1,trackname2,mode2,...
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=refGene,full,gc5Base,show
note	currently, 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 name	metadata
value	metadata terms joined by comma, space in term names must be coded as %20
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&metadata=Histone%20Mark,12003
note	none-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 name	custombedgraph
value	name1,url1,name2,url2,...
example	http://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
note	special characters in the names must be escaped

To add custom bigWig track

parameter name	custombigwig
value	name1,url1,name2,url2,...
example	http://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
note	special characters in the names must be escaped

To add custom bed track (positional annotations)

parameter name	custombed
value	name1,url1,mode1,name2,url2,mode2,...
example	http://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
note	mode must be one of "thin", "full", "density" special characters in the names must be escaped

To add custom long-range interaction track

parameter name	customlongrange
value	name1,url1,mode1,name2,url2,mode2,....
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&customlongrange=trackname,http://vizhub.wustl.edu/hubSample/hg19/K562POL2.gz,arc
note	mode 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 name	custombam
value	name1,url1,mode1,name2,url2,mode2,...
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&custombam=tempest,http://vizhub.wustl.edu/hubSample/hg19/bam1.bam,density
note	mode can be one of "thin", "full", "density" special characters in the names must be escaped

To show secondary panel (experimental)

parameter name	splinters
value	coordinate (e.g. chr5:5000000-5100000)
example	http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gc5Base,show&splinters=chr5:5000000-5100000
note	multiple 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 name	defaultContent
value	string "on"
example	http://epigenomegateway.wustl.edu/browser/?genome=hg18&defaultContent=on
note