Vista tracks on genome browser

[Hani Alotaibi]

Hi,

I have been trying to display the vista tracks on the genome browser with no success. I used to do this with no problem, but lately no.

I am using Safari on a MacOSX6 machine, but I have tried different browsers like firefox and camino with similar results.

Could you please suggest a solution?

Thanks

Hani Alotaibi

[Brooke Rhead]

Hi Hani,

Can you describe what steps you are taking to view the track and what
kind of result/error you are seeing? I turned on the "Vista Enhancers"
track on the hg19, hg18, and hg17 genome browsers just now, and I could
not see a problem.

I do note that the data on the tracks is rather sparse -- I had to zoom
out a few times from the default positions to see any items in the track.

Please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

[Hani Alotaibi]

Dear Brook,
Thanks for the quick response,
I would like to display multiple genome alignments from the vista tools
website on the Ucsc genome browser. Usually i use the mouse genome as the
base sequence.
I start from the vista tools page at http://genome.lbl.gov/vista/index.shtml

And from the menu i select browser, then i select the mouse genome, write the
chromosome coordinates, and then select VISTA tracks on UCSC Browser, then
click submit. This takes me to the Genome browser at Ucsc, with a custom
track displaying conserved regions in multiple genomes. The current problem
is not being able to see the conservation peaks.
I can add my own custom tracks though.
And i can see the vista track menu with several options, but not on image.
I hope this was clear.
Thanks for the effort.
Looking forward your reply,
Sincerely
Hani alotaibi

On Fri, 07 Sep 2012 11:19:32 -0700 Brooke Rhead <rh...@soe.ucsc.edu> wrote:
> Hi Hani,
>
> Can you describe what steps you are taking to view the track and what
> kind of result/error you are seeing? I turned on the "Vista Enhancers"
> track on the hg19, hg18, and hg17 genome browsers just now, and I could
> not see a problem.
>
> I do note that the data on the tracks is rather sparse -- I had to zoom
> out a few times from the default positions to see any items in the track.
>

> Please reply to gen...@soe.ucsc.edu.Brooke Rhead

[Brooke Rhead]

Hi Hani,

Thank you for the clear explanation. I can reproduce the problem here.
It looks like the steps outlined below actually take me to a mirror of
the Genome Browser, at http://pipeline.lbl.gov/cgi-bin/vistatrack,
rather than to our official site at
http://genome.ucsc.edu/cgi-bin/hgTracks. (It is odd, though, that every
link on the pipeline.lbl.gov page goes back to our site at
genome.ucsc.edu . . . usually all of the links on our mirror sites go to
the mirror's domain. Perhaps this mirror is set up in a non-standard way.)

I don't think there is anything to do on our end to correct the problem.
I suggest contacting the Vista group directly:
http://genome.lbl.gov/vista/contact.shtml.

--

Brooke Rhead
UCSC Genome Bioinformatics Group