Getting Genome Browser

Using JavaScript version

Using Polymer web component

To facilitate the use of the Genome Browser component, a WebComponent has been created that you can import into your html page.
In this tutorial you will learn how use this component for visualizate differents tracks.

In first time, you must import the component in your page.

<link rel="import" href="jsorolla/dist/core/webcomponent/genome-browser.html">

Subsequently, we will declare the genome component browser in our html code.  For this we must know the list of parameters that the component accepts.

Here is a list of parameters that the component accepts and uses:

To use opencga webservices, you will need to know which project the data to display.

Species to draw. Default: homo sapiens.

Enables or disables the component. If it is disabled the component will not be displayed.

Default: false.

This parameter sets other settings of the genome maps that the user wants to pass.

Finally, declare the component. In this case, we only defined the GeneTrack and Sequence track:

 <genome-browser cellbase-client="{{cellbaseClient}}" region="{{region}}" tracks="{{tracks}}" active="true">
 </genome-browser>

In the javascript part we will give value to the variables:

			CELLBASE_HOST = "bioinfo.hpc.cam.ac.uk/cellbase";
            CELLBASE_VERSION = "v4";

            let cellBaseClientConfig = new CellBaseClientConfig(CELLBASE_HOST, CELLBASE_VERSION);
            this.cellbaseClient = new CellBaseClient(cellBaseClientConfig);

           	this.region = new Region({chromosome: "11", start: 68177378, end: 68177510});
            this.tracks ={sequence: {type: "sequence"}, gene: {type: "gene"}};

We have created a cellbase client that will connect to the Host, "bioinfo.hpc.cam.ac.uk/cellbase".

If we do not want to change the installation of cellbase, it is not necessary that we define the host and the version, but we initialize a client.

With the parameter "region", we ask that the display is at 11: 68177378-68177510. It's possible to not see these positions in the display where the painted region is shown, 

but you wil see a window frame containing the region. This is because the genome browser adjusts the display to optimize the cache. 

Finally, the last param is "tracks", in this case we want see the track "sequence" and "gene". We can define other types of tracks as follows:

• Individual Variant Track (for example SNP): {trackname:{type:"variant", config:{}}}.
• Family Variant Track: {trackname:{type:"variant", config:{samples:"sample1","sample2"}}}.
• Aligment Track: {trackname:{type:"alignment", config:{files:"bam1","bam2"}}}