How to pass coordinates to a public session?

[Bert Gold]

Hi!

I am using GBiB and enjoying it.

Now I have created a session at a particular location in hg19 and

want to permit others to load new coordinates into that session (using

the same settings).  I realize I can save the settings as a flat file and

have done so.

There are three lines of coordinates in the settings file:

viz-

.....line 26 of settings file....

knownGene.label.gene 1

lastPosition chr7:117199330-117199900

lastVirtModeExtraState 

lastVirtModeType default

oldPosition chr7:117199330-117199900

org Human

position chr7:117199330-117199900

...line 34 of settings file...

So, my question for you is, using either the URL method or the attachment

method, what do I have to pass to the browser session (and how do I do it),

to open it at say, chr9:34,649,292-34,649,692 instead of the chromosome 7 coordinates given above.  I want same settings, different coordinates.

Thank you for any insight.

Bert Gold

knownGene.label.gene 1

lastPosition chr7:117199330-117199900

lastVirtModeExtraState

...a coupla lines later...

Bert Gold, MB(ASCP)CM, Ph.D., FACMGG, CGMBS  

Senior Clinical Molecular Geneticist

Natera, Inc.

201 Industrial Rd

San Carlos, California

EMAIL: bg...@natera.com

OFFICE: (650) 249-9090 extension 1537

CELL: (302) 507-1827

[Matthew Speir]

Hi Bert,

Thank you for your question about using sessions in the UCSC Genome Browser.

There should be no need to modify the session file. All you need to do is add the "position=<chr_position>" parameter to your URLs. For example, here is a session that opens up a region on chr9 in the human assembly hg38:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_NAR_2016_Fig1.

If we add this "position" parameter to the URL like so:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_NAR_2016_Fig1&position=chrX:154762756-154777689

You will see that it now loads a position on chrX.

However, if you do want to continue with your plan to change the session settings file, you would just need to change the "position" line. So, for your example, if you wanted the session to load to the position on chrX I linked above, this line would become:

position chrX:154762756-154777689

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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