URL Parameters

URL parameter works in this way:

https://proteinpaint.stjude.org/?genome=hg19&gene=ALK&dataset=pediatric

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.

"gene"

Generates view for a gene. Example:

https://proteinpaint.stjude.org/?genome=hg19&gene=ALK&dataset=clinvar

• Display a gene by given name. Value can be gene symbol or isoform accession, value is case-insensitive
• Requires ”genome”

• 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:

    • https://proteinpaint.stjude.org/?genome=hg19&gene=ALK&dataset=pediatric

  • 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

    • Example:

      • https://proteinpaint.stjude.org/?genome=hg19&gene=ALK&dataset=pediatric&hlaachange=G574R,F1174L
• All types of custom track parameters can be used as well, as defined in the “block” section below.

block

Launches a genome browser. Example:

https://proteinpaint.stjude.org/?block=on&genome=hg19&position=chr17:7568451-7591984&bigwigurl=UCSC_phyloP,http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP100way/hg19.100way.phyloP100way.bw

genome

Required. Provides reference genome name.

Genomic regions

Optional. Specify genomic regions.

position

• Coordinates are 0-based, example

  • ?block=on&genome=hg19&position=chr1:1234-5678

regions

• Using ”regions” to join more than 1 region by comma

  • ?block=on&genome=hg19&regions=chr1:111-222,chr2:333-444
• There is a bug of incorrect genomic ruler rendering when providing multiple regions.

hlregion

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.

Tracks

Optional. There is no parameter called “tracks”, but many different parameters to provide different types of tracks.

bigwigfile

bigwigurl

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

• Example

  • ?bigwigfile=[name1],[path/to/file1.bw],[name2],[path/to/file2.bw],....
  • ?bigwigurl=[name1],[url1],[name2],[url2]
• Note that this method won’t allow setting Y scale or other configurations

vcffile

vcfurl

Provide one or more VCF tracks. Requires VCF 4.2 format. Each in the form of “name,path-or-url”, all joined by comma.

URL format:

?vcffile=[name1],[path/to/file1],...
?vcfurl=[name1],[path/to/url1],...

Example:

junctionfile

junctionurl

Provide one or more junction tracks, see junction file format. Each in the form of “name,path-or-url”, all joined by comma.

URL format:

?junctionfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],....

Note that this method won’t allow configuring the junction type.

mdsjunctionfile

“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.

URL format:

?mdsjunctionfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],....

bedjfile

bedjurl

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.

bampilefile

bampile file format

?bampilefile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],...

aicheckfile

aicheck file format

?aicheckfile=[name1],[path/to/file1.gz],[name2],[path/to/file2.gz],...

svcnvfpkmurl

svcnvfpkmfile

Manuscript in prep… will add user tutorial later.

Submits a custom GenomePaint track, must have the “svcnv” file. FPKM and VCF files are optional.

URL format:

?svcnvfpkmurl=[track_name],svcnv,[URL to svcnv.gz file],fpkm,[URL to fpkm.gz file],vcf,[URL to vcf.gz file]

mds

Manuscript in prep…

Launches an official GenomePaint track.

URL format:

?mds=[dataset_label],[query_key]

study

Loads a study using the JSON file location.

URL format:

?study=path/to/mystudy.json

On PP server, the corresponding file is /path/to/mystudy.json

View this tutorial on how to organize data into a study.