Loading Ucsc Custom Track Automatically

Question

[Rossella]

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

[Sukhi Singh]

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.

[Rossella]

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

[Pascal]

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

[Rossella]

Perfect, that is exactly what I needed

[nonish5]

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!

Answer 1

[Sukhi Singh]

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/

Answer 2

[Maximilian Haeussler]

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

Answer 3

[Istvan Albert]

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.