URL parameter works in this way:
It generates links of customized views that can be bookmarked or published.
URL parameters consist of "key=value" pairs. The keys are listed below, they are case-insensitive.
Generates view for a gene. Example:
Display a gene by given name. Value can be gene symbol or isoform accession, value is case-insensitive
Optionally, specify built-in datasets using parameter "dataset":
If more than 1, join by comma
Dataset must be hosted on the PP server
Value is case-insensitive
Example to load the "Pediatric" dataset:
When using datasets, highlight certain mutations matching with given name
Effect: any groups of mutation showing a match with the given name will be shown as expanded. All the rest of groups are folded.
This feature is only intended for point mutation AA change name. The provided name must exactly match with the content in the DB or VCF file
All types of custom track parameters can be used as well, as defined in the "block" section below.
Launches a genome browser. Example:
Required. Provides reference genome name.
Optional. Specify genomic regions.
Coordinates are 0-based, example
Using "regions" to join more than 1 region by comma
There is a bug of incorrect genomic ruler rendering when providing multiple regions.
Optional. Provide one or more regions to highlight. Each region is in the format of "chr:start-stop". Do not use commas in start or stop positions. Join multiple regions by comma.
There is a bug that it will highlight regions that are outside of view range.
Optional. There is no parameter called "tracks", but many different parameters to provide different types of tracks.
To provide "bigWig" tracks. Learn how to generate a bigWig file
Provide one or more bigwig tracks, each in the form of "name,path-or-url", all joined by comma. When using file, the files are hosted in the
directory of the ProteinPaint server
Note that this method won't allow setting Y scale or other configurations
Provide one or more VCF tracks. Requires VCF 4.2 format. Each in the form of "name,path-or-url", all joined by comma.
Provide one or more junction tracks, see junction file format. Each in the form of "name,path-or-url", all joined by comma.
Note that this method won't allow configuring the junction type.
"MDS junction" track is the v2.0 of the junction track, work-in-progress. This parameter will provide one or more tracks, the file of which are hosted on the ProteinPaint server.
Provide one or more JSON-BED tracks, see JSON-BED file format. Each in the form of "name,path-or-url", all joined by comma.
Manuscript in prep... will add user tutorial later.
Submits a custom GenomePaint track, must have the "svcnv" file. FPKM and VCF files are optional.
?svcnvfpkmurl=[track_name],svcnv,[URL to svcnv.gz file],fpkm,[URL to fpkm.gz file],vcf,[URL to vcf.gz file]
Manuscript in prep...
Launches an official GenomePaint track.
Loads a study using the JSON file location.
On PP server, the corresponding file is
View this tutorial on how to organize data into a study.