Question: Loading Ucsc Custom Track Automatically
2
gravatar for Rossella
3.3 years ago by
Rossella330
Rossella330 wrote:

Hi, is there a way of loading a ucsc genome browser track automatically from a script (preferably in python but any language would do) so that a user invoking the script can directly see the visualization with the loaded track?

Thanks a lot in advance

ADD COMMENTlink modified 10 months ago by Maximilian Haeussler1.1k • written 3.3 years ago by Rossella330

Can elaborate more, you want a script to invoke a ucsc instance in a browser, with your own track?? Make a text file with a bigwig track information, save it on your http enabled web server and load into ucsc via a link.

ADD REPLYlink written 3.3 years ago by Sukhdeep Singh6.0k

Can you show me how to load it via a link? I couldn't find an explanation on how to do it and that would be the best solution for me. I already have a script to create the track file, now I just need a way to load it automatically and direct the user to the page with the loaded track. Thanks

ADD REPLYlink written 3.3 years ago by Rossella330
1

You can find all you need here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK

As mentioned before, just generate a text file with your custom tracks. You can also add options about other tracks. Here is an example:

browser hide all browser pack knownGene refGene ensGene acembly browser dense est track name='Your custom track' description='best annotation ever' type='bigBed' bigDataUrl='http://yoururl.com/annotation.bb' db='mm9' visibility='pack'

Upload this to your web server. Then use the following URL:

http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&hgt.customText=http://yoururl.com/tracks.txt&db=mm9&position=chr4:107816815-107817581

This would lead to the position chr4:107816815-107817581 on mm9. Your custom track would be shown in "pack", knownGene, refGene, ensGene, and acembly too. ESTs in 'dense' and all other tracks are hidden.

Pascal

ADD REPLYlink written 3.3 years ago by Pascal220

Perfect, that is exactly what I needed

ADD REPLYlink written 3.3 years ago by Rossella330

Hi, 

Is this possible also for presenting a bedGraph format? 

I read the documentation but couldn't make it work with "url" instead of "bigDataUrl".

Thanks!

 

ADD REPLYlink written 9 months ago by nonish520
2
gravatar for Sukhdeep Singh
3.3 years ago by
Sukhdeep Singh6.0k
Germany
Sukhdeep Singh6.0k wrote:

Hi,

Check this I just wrote a tutorial on how to do it. Of course, you can automate to any level. I also included how to it within R. http://www.biostars.org/post/show/42844/visualizing-chip-seq-data-using-ucsc-bigwig/

ADD COMMENTlink written 3.3 years ago by Sukhdeep Singh6.0k
1
gravatar for Maximilian Haeussler
10 months ago by
UCSC
Maximilian Haeussler1.1k wrote:

This has been posted years ago, just in case that someone comes across it today: Please do not http-post custom tracks anymore from external apps into the UCSC website. It's a lot easier to create a track hub and load it via the hubUrl parameter. See the documentation at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Session

ADD COMMENTlink written 10 months ago by Maximilian Haeussler1.1k
0
gravatar for Istvan Albert
3.3 years ago by
Istvan Albert ♦♦ 56k
University Park, USA
Istvan Albert ♦♦ 56k wrote:

Doing it in python is not particularly difficult, you can use directly urrlib or alternatively use something like twill to automate web scripting.

At the same time as an alternative you might want to look at Track Hubs

ADD COMMENTlink written 3.3 years ago by Istvan Albert ♦♦ 56k
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