Re: UCSC Genome Browser Download Help
Ann Zweig
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Ann Zweig
Engineering & Project Manager
UCSC Genome Browser
http://genome.ucsc.edu
UC Santa Cruz Genomics Institute
http://genomics.ucsc.edu
Hi Dr. Zweig,
I was hoping you could help me with downloading images from the genome browser (or forward this email to anyone who can). I want to download a large image of an entire gene (hEDN1) at the base level. I want to print it on a poster so we can look at transcription factor binding etc. The only things I have found would allow me to download a pdf of the current browser image but that only a few hundred base pairs at a time. Is there any way to download the whole gene even if I can't see it all in the browser at once? Thanks so much!
Brian Lee
Dear Kristen,
Thank you for using the UCSC Genome Browser and your question about creating an image at the base level for an entire gene.
There is no easy direct way to achieve what you are attempting. Under the top Genome Browser menu there is a Configure option that allows you to change the "image width" to a higher number of pixels. When the screen is stretched wide enough, the DNA bases will display, however, there are limits of what can be viewed, about 5,000 pixels on our public site. On our development machine, genome-test, the limits are about 25,600 pixels.
Here is a session on our genome-test site where I have stretched the pixels to 25,000 and also invoked the "multi-region" mode that only displays exons, condensing the display of the EDN1 gene: http://genome-test.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.EDN1.pixels
In this case I have used the multi-region mode to turn off splice variants, you may be interested in a different transcript of EDN1, by going to the "UCSC Genes" track and clicking "splice variants" you can get different transcripts to display, or you could use the mult-region custom regions approach to slice the genome into defined desired coordinates. Please read more about multi-region here, http://genome-test.soe.ucsc.edu/goldenPath/help/multiRegionHelp.html, you can quickly turn in on and off by using "e v" to go to exon view and "d v" to return to default view. There is also an option under the View menu.
By going to the View ->PDF/PS menu the attached image was created by clicking the EPS option to "Download the current browser graphic in EPS" (I renamed the image EDN1.eps).
Thank you again for your inquiry and using the UCSC Genome Browser, I hope this is useful. You may be interested including some of our transcription factor binding tracks, here is another session with some of those displayed: http://genome-test.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.EDN1.tfbs
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.
All the best,
Brian Lee
UCSC Genomics Institute
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