[Genome] lost track entries / multiple configurations

[Rachel Harte]

Hello Micha,

If you have a large number of items in the same location, then the code
will not allow display of all the data. We see this sometimes with ESTs
and with chain tracks and also the SAGEtags in the ENCODE data on hg17.
If you set visibility to dense for the custom track, then you will be able
to view all the data collapsed into one item.

What type of data are you loading? Is there a way that you can reduce the
data in any way or maybe load the data in more than one track. The data is
still available but you can not view it all. All of the data will be
accessible in the Table Browser so you would still be able to query it
there and intersect it with other tracks.

With regard to your question about conflicting parameters from different
sources, if you add a line to a custom track, then this just gives the
default position for loading that track which will stay the same. So whenever
you go to the custom track manager and select to view a custom track then it
will take you to its default position (if specified) otherwise to the
position of the first item with the default visibility. Once viewing the
Genome Browser, you can change the visibility using the track control for
the custom track. The assembly information is also retained so
if you created the track on hg18 (Mar 2006), then it will only appear on
hg18 and you would need to select hg18 in the custom track manager or the
hg18 Genome Browser in order to view the custom track.

If you change the database to say mouse mm8 in the URL, then it will take
you to the mm8 Genome Browser. The organism and assembly information
variables are kept in the cart, and this means that if you have just
visited mm8 and then choose Blat or the Table Browser or Gene Sorter, then
mm8 will be the default organism. Other variables from the URL and some that
you do not see including the tracks' visibilities and the genome position
are also kept in the cart. So if you go back to a Genome Browser for an
assembly then you will see the same tracks and position as when you last
visited that assembly. These settings are associated with an id (hgsid) which
you will see appearing in the URL. You can reset everything to default using
the "Click here to reset" on the Genomes Gateway page (click on the "Genomes"
link on the top blue bar). This will also remove any custom tracks
that you added. You can see all these settings in the cart by doing a cart
dump: http://genome.ucsc.edu/cgi-bin/cartDump.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics
Group http://genome.ucsc.edu


On Thu, 31 May 2007, Micha Sammeth wrote:

> Hi,
>
> I have two questions:
>
>     - if you display too many data in a track in the browser it seems to
> cut the lasts entries, displaying a line: "Last row XX:"
> I guess this is due to limit the resources, I couldnt find a way to
> deactivate it. Is there any way to get information about the cut entries?
>
>     - what happens if you submit the browser contradicting information
> via different sources? For instance you can set region, track display
> features, ... via the URL with which you call the browser, but at the
> same time, you may specify these parameters in the browser configuration
> of a dynamically loaded custom track. Which configuration overrides
> which, is there an order to the processing?
>
>
> Thank you !! micha.
>
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