Question: How To Integrate Mirror Ucsc Genome Browser Into Local Web Service
1
gravatar for liqingyan
6.1 years ago by
liqingyan20
china/guangdong/sysu
liqingyan20 wrote:

I want to develop a web site with a function to show WIG data visually by using existing genome browser. for example: there is a page in my site, showing some database records, and I want to add some genome browser in this page to show WIG data visually.

  1. UCSC genome browser is preferred, but how to integrate it to our web service.

  2. Please recommend some other genome browser that can integrate easily.

Thanks for your help.

genome ucsc browser • 2.4k views
ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by liqingyan20
1
gravatar for Giovanni M Dall'Olio
6.1 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

A solution that can be implemented in a short time and doesn't require too much maintenance is the UCSC Tracks Hubs.

Basically, you create your (big)Wig files and store them to a webserver. Then, people will be able to access to the tracks from any other UCSC browser installation (e.g. the one at UCSC), by adding a parameter to the URL. See this example of a UCSC Hub: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt

This solution is quick and easy, and you do not have to setup and configure a custom UCSC instance. Moreover, people will be able to use it from any other browser installation, and and compare it with their own datasets. However, I don't know exactly what you mean by "integrating the browser in your web service", and which type of web services you are developing, so I am not sure if this is useful for you.

P.s. even if you do not use track Hubs, have a look at the Track Hubs Database Definition document, which I think is the best documentation available for defining tracks in UCSC.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Giovanni M Dall'Olio26k

Yeah, I was also going to suggest this was the way to go. The hubs are a nice solution for exactly this issue.

ADD REPLYlink written 6.1 years ago by Mary11k
0
gravatar for Sandeep
6.1 years ago by
Sandeep250
Manipal, India
Sandeep250 wrote:

I have never tried it myself but I came across this http://genomewiki.ucsc.edu/index.php/Main_Page.

There is detailed instructions to mirror UCSC browser.

Hope this helps

ADD COMMENTlink written 6.1 years ago by Sandeep250
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