Custom multi-region View without web server

[Natalie Jameson Kiesling]

Hello, 

I would like to use the "Custom regions from BED URL" setting in the genome browser under multi-view. It looks to me that in order to supply a BED URL it will be necessary to create a Track Hub. 

Is that correct? If so, is there another way to upload a BED file into multi-view without having to get the track from a web server?

Thank you, 

Natalie

______________________________

Natalie Kiesling, Ph.D.
Scientist I
Progenity, Inc.

5230 S. State Road
Ann Arbor, MI 48108
www.progenity.com

[Brian Lee]

Dear Natalie,

Thank you for using the UCSC Genome Browser and your question about using the custom regions from a BED URL for the multi-view feature.

You do not require a track hub to use this feature, but currently there is a need for a web server that can provide text file information over the internet that can be uploaded to the browser, in the future we plan to enhance this feature to allow other ways to upload regions. There are some examples on the Multi-Region User Guide Page (accessible by clicking the "help" link when viewing the "Configure Multi-Region View" pop-up): http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html

In the Custom Regions Mode section you will see the start of of a example BED3 file,http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#CustomRegions, and also a link to "Example 3. Custom Regions from BED file" lower on the page. There you will find a link to a "BED file" for mm10 that you can load on the mm10 browser:http://genome.ucsc.edu/goldenPath/help/examples/mm10multiRegionexample.txt

There is also a link there to click that will show a session of these regions using these regions in the Multi-Region tool:http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/bed3Session.txt

Please note that you can simultaneously load a multi-region BED URL as a custom track and set it to full (seen as "User Supplied Track" line in image with names like "block1, block2, block3...") so you can have annotations about the slices you are providing. You can also further provide more complicated BED information using BED12 which will allow for defining exon blocks (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

Going back to the question regarding having an internet location to serve files, you may wish to contact your institution to learn if you can have an internet accessible folder to place files, it is very likely your system administrators are willing to provide this. Also, when just serving text files, many free online file sharing resource tools will work such as git hub or instituting public sharing or folders from goolge drive or drop box, but since these services are constantly changing, we can not provide guidance about using them (and they will not work for byte-range requests needed for non-text binary files such as used in Track Hubs).

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply toge...@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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