Question: Loading UCSC custom track automatically
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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
2 answers
2
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/
0
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
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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.
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
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
Perfect, that is exactly what I needed