URL parameter specification (effective v13)

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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

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