Genome Browser

[Venicio Antunes de Sá]

Hi,

I'm doing my MS in UFPR(Universidade Federal of Paraná) in Bioinformatic, my tesis is build one web app for RNA-seq analise with R as back end. Can I use your genome browser in my app? Does it have one API or webserver to be used in my APP ?

Regards,

Venicio A. Sa

[Jonathan Casper]

Hello Venicio,

Thank you for your question about using our browser in your web app. We do not have an API to interact with our webserver, but you are welcome to build an app. Please note that we have many users, so we must block heavy use of our web resources. If your app only needs to access our CGIs once every 15 seconds or so, that is fine. If you need much more than that, we suggest that you try another approach. One option is to download track data from our download server at http://hgdownload.soe.ucsc.edu. You can then access that data directly. Another option, if you need to interact with a webserver, is to download our Genome Browser in a Box (GBiB), and use that as the webserver instead of our main site. More information about GBiB is available at http://genome.ucsc.edu/goldenPath/help/gbib.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Jonathan Casper]

Hello Venicio,

One of our engineers also suggests that you might find the hgRenderTracks (http://genome.ucsc.edu/cgi-bin/hgRenderTracks) useful. hgRenderTracks returns only the track image for the current genome position, so it's a bit easier to use if the track image is all that you want. Please note that the only way to change coordinates with hgRenderTracks is via the URL (e.g., http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr2:20000-30000). More information about constructing links like this is available in our linking FAQ at http://genome.ucsc.edu/FAQ/FAQlink.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group