URL parameter

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URL parameters can be used to perform tasks such as adding tracks, defining view range. They consist powerful "shorthands" to configure browser and show customized contents, without having to rely on sessions (which are saved on the browser server and could be deleted!) or datahub files, though with limited capability.

See the Gallery for many applications of URL parameter.

All the keywords used for URL parameters are case insensitive. Contents from this blog post (http://washugb.blogspot.com/2012/12/url-parameter-specification-effective.html) will be moved here.

genome

Value is name of the reference genome.

&genome=hg19

defaultcontent

coordinate

A variety of coordinate formats can be used to define view range:

  1. single basepair: &coordinate=chr1:5932545
  2. region: &coordinate=chr1:3333-44444

session

bedgraph

To submit one or more bedGraph format tracks.

Value: Name,URL,Name2,URL2,... Join fields by comma.

Backward-compatible with the "custombedgraph" keyword.

bigwig

To submit one or more bigWig format tracks.

Value: Name,URL,Name2,URL2,... Join fields by comma.

Backward-compatible with the "custombigwig" keyword.

bed

To submit one or more Bed format tracks.

Value: Name,URL,mode,Name2,URL2,mode2,... Join fields by comma.

Value of "mode" must be one of: "full", "thin", "density"

Backward-compatible with the "custombed" keyword.

This format is deprecated, consider using Hammock format instead.

longrange

To submit one or more long-range chromatin interaction format tracks.

Value: Name,URL,mode,Name2,URL2,mode2,... Join fields by comma.

"Mode" must be one of: "full", "thin", "density", "arc", "trihm".

Backward-compatible with the "customlongrange" keyword.

bam

To submit one or more bam tracks.

Value: Name,URL,mode,Name2,URL2,mode2,... Join fields by comma.

Value of "mode" must be one of: "full", "thin", "density"

Backward-compatible with the "custombam" keyword.

gftk

publichub

To load one or more public hubs with their ID. The ID must be registered in the "id" field of a public hub definition. Join multiple IDs by comma.

&publichub=datasetA,datasetB

hammock

To submit hammock tracks. See here: Hammock#From_URL_parameter

splinters

To add one or more parallel panels. A valid coordinate string must be given to activate a panel. Coordinate string must be in the form of chromosome:start-stop.

&splinters=chr1:111-222,chr2:333-444

datahub

To load one JSON datahubs with their URLs.

&datahub=http://host/path/to/myhub.json

Backward compatible with keyword "datahub_jsonfile".

tknamewidth

Set track name width (the white space to the left of track images where track names are shown).

&tknamewidth=100

tkwidth

Set track width (the central panel, minimal requirement is 800).

&tkwidth=800