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 |
