Thursday, December 27, 2012

URL parameter specification (effective v13)

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
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 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