xQTL GBrowse integration

Desired behavior:

• As a user I want to view Marker and Probe on the genome (= annotations)
• As a user I want to view QTL on the genome (= data set)
• As a user I want to view genotypes per strain on the genome (= data set)
• As a user I want to view gene expressions per individual on the genome (= data set)

Proposed solution:

• Per chromosome and per annotation produce a BED file, e.g. for all markers on ChrI
• Per chromosome and per data set produce a WIG file, e.g. for QTL profiles on ChrI
• Include in xQTL suitable links towards the gBrowse instance that include loading of the proper BED / WIG file(s) as custom track
• Include in these files hyperlinks back to the molgenis instance that serves them

We can cache these files so we don't need to update all the time.

In case data sizes become an issue we should produce BigBed? and BigWig? files. See ​http://bioinformatics.oxfordjournals.org/content/26/17/2204.full.pdf

How to add GBrowse linkouts to MOLGENIS databases

Add a query option to the 'rubberband' menu where you can drag to select a genomic region

Open your GBrowse *.conf file. The rubberband menu has HTML elements and looks like this:

[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr>
           <th style="background:lightgrey;cell-padding:5">
             SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
                   onclick="SelectArea.prototype.cancelRubber()">
               [X]
             </span>
           </th>
         </tr>

We add a table row with the linkout to a URL like this:

<tr>
  <td onmouseup="SelectArea.prototype.cancelRubber()">
    <a href="http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=SELECTION" target="_BLANK">
    molgenis region query
    </a>
  </td>
</tr>

The value of SELECTION is a GBrowse notation, so the accepting service must be compatible with these requests. An example of a resulting request:

.../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999

At the moment there is no MolgenisService? to facility this, but it the principles are trivial. ​A first step was done to enhance the existing filters for this purpose, but this is not GBrowse syntax yet. The multifilters ​are used like this.

Add a popup balloon to an annotation track

Open your GBrowse *.conf file. In the track, which e.g. looks like this:

[hxb-sdp]
feature       = experimental_feature:hxb_sdp
database      = variations

We add a balloon property, with a hyperlink, like this:

balloon click = <h2>Marker $name</h2>
       <a href='http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=$id'>Marker info from molgenis</a><br>

When clicking this link, it will request a marker by ID. The correct mapping for the $-variable to MOLGENIS entity attribute should be investigated on a per-database basis.

.../api/find/org.molgenis.xgap.Marker?name=1

Online GBrowse at GWAS Central (HGV-Base)

​http://www.gwascentral.org/browser/genome?r=HGVRS1375,HGVRS1374,HGVRS1373&t=

Online GBrowse at WormBase

​http://www.wormbase.org/db/gb2/gbrowse/c_elegans/?name=I:10747696..10779324