Question: Loading Ucsc Custom Track Automatically
1
gravatar for Rossella
2.0 years ago by
Rossella320
Rossella320 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 written 2.0 years ago by Rossella320

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 2.0 years ago by Sukhdeep Singh4.6k

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 2.0 years ago by Rossella320
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 2.0 years ago by Pascal160

Perfect, that is exactly what I needed

ADD REPLYlink written 2.0 years ago by Rossella320
2
gravatar for Sukhdeep Singh
2.0 years ago by
Sukhdeep Singh4.6k
Germany
Sukhdeep Singh4.6k 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 2.0 years ago by Sukhdeep Singh4.6k
0
gravatar for Istvan Albert
2.0 years ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k 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 2.0 years ago by Istvan Albert ♦♦ 39k
Please log in to add an answer.

Help
Access
  • RSS
  • Stats
  • API

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.0.0
Traffic: 881 users visited in the last hour