Programmatically generate browser images

[Vince Forgetta]

Hi,

Is there a method and usage policy on how to programmatically access the UCSC Genome Browser to generate browser images?

I would like to embed PNG images of the UCSC Genome Browser with plots I am generating. I was thinking along the lines of somehow using browser lines to specify the genome position and layout of tracks and submit this via URL or some other method to UCSC Browser.

Thanks,

Vince

[Luvina Guruvadoo]

Hello Vince,

Thank you for your question and my apologies for the late reply. One of our engineers looked into this and provided the following comments: if you only need the image, and nothing else from the page, then it probably would be a little more efficient to use hgRenderTracks. However, please keep in mind we do have limits on the number of hits to our server, see http://genome.ucsc.edu/FAQ/FAQdownloads.html#download2. If you are running some CGI web-service thing where you cannot control how many hits and requests are coming in per second, it would be better for you to run your own local instance of the browser (our Genome Browser in a Box) and fetch from that. More info on the Genome Browser in a Box can be found here: https://genome.ucsc.edu/goldenpath/help/gbib.html.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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[Vince Forgetta]

Thanks Luvina, and thanks to the engineer who looked into this as well.

Initial plan would be to use this within R to generate a UCSC Genome Browser image (few Mbp max) and add a plot in R above it of the corresponding genomic region.  Would be for internal use initially.  Should it expand beyond our lab I will definitely contact you all again to confirm what best strategy is given the implementation I have developed.

Vince