Removing custom tracks

[Brad Davis]

I was wondering if it is possible to remove custom tracks that had been previously added to the UCSC browser in the current session?  I found a post about using the &hgct_doRemoveCustomTrack=1&hgct_table=ct_boo command, but I cannot get it to work.  The post describing this functionality is from 2007 so I was wondering if this function had been removed, or if some other function had been added in it’s place?  If it still exists, can I be pointed in the direction of the documentation for this?

Thanks,
Brad davis

[Brooke Rhead]

Hi Brad,

I believe you are referring to this post:
https://lists.soe.ucsc.edu/pipermail/genome/2007-June/013739.html. The
basic functionality is still the same, but the actual "table name" (the
name assigned to the table in our system when you upload it) now has a
number appended to it. You can find the number by selecting the track
in the Table Browser. A track named "boo" will now have a name along
the lines of "ct_boo_4677".

It looks like the name of the database (the db= parameter) is also
needed when removing a custom track via URL. So, for instance, your URL
could look something like this:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgct_doRemoveCustomTrack=1&hgct_table=ct_boo_4677

Another way to get rid of all custom tracks (and all settings) via URL
is to use the "cartReset" CGI, like this:

http://genome.ucsc.edu/cgi-bin/cartReset

I hope this information is helpful. If you have further questions,
please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 5/1/13 11:20 AM, Brad Davis wrote:
> I was wondering if it is possible to remove custom tracks that had been
> previously added to the UCSC browser in the current session? I found a
> post about using the &hgct_doRemoveCustomTrack=1&hgct_table=ct_boo
> command, but I cannot get it to work. The post describing this

> functionality is from 2007 so Iwas wondering if this function had been
> removed, or if some other function had been added in it�s place? If it

> still exists, can I be pointed in the direction of the documentation for
> this?
>
> Thanks,
> Brad davis
>

> --
>
>
>

[Brad Davis]

Hello,

How would I look up what the number from the track is in an automated
fashion? Can it be done with an HTTP request? I am trying to automate the
removal of tracks.

Thanks,
Brad

>> removed, or if some other function had been added in it¹s place? If it

[Brooke Rhead]

Hi Brad,

I spoke to our developers, and there aren't any straightforward ways to
find the custom track number. There might be an easier way to
accomplish your goal, though. You could potentially use a track hub
instead, which would allow you to control the contents of the hub and
make changes to it without interacting with the Genome Browser at all
(see http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html for more
info). Alternatively, perhaps you could use a saved session
(http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html); for
instance, we have an FAQ that describes how to link to specific tracks
in the Genome Browser using a saved session with all tracks hidden:
http://genome.ucsc.edu/FAQ/FAQlink.html#link4.

What is your usage scenario? Maybe we can suggest some alternatives.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

[Brad Davis]

Hello Brooke,

We are building an epigenome portal to allow users to view the reference
epigenomes being created at the BC Cancer Agency. It is similar in function
to the Epigenome Roadmap Atlas. Currently when a user selects a set tracks
they want to visualize the track information is written to a hub file at a
internet accessible address and this hub file (e.g.
http://edccwashu.bcgsc.ca/hubs/hub.ucsc.Thu-May--2-04-27-39-2013.wmS5iRPtf0)
is then transmitted as part of the HTTP request to the UCSC browser. The
issue is that if a user selects a track decides to visualize it and then
comes back to the table and unselects a track, the track continues to be
displayed on the genome browser. I understand that the user can remove the
track from their display using the manage tracks feature of the UCSC
browser, but I was hoping to make our table a little bit more transparent to
for users. The manage tracks tool is great, but I am aiming to make as few
assumptions about the users understanding of genome browsers as possible.
Admittedly any experienced user will be familiar with them, but I would like
to not have to make that assumption. I know that there is a feature which
allows for all of the tracks to be removed as a group, but that goes too
far. I can imagine a scenario where a user has loaded their own tracks
manually (or via some other genomics data center) and then comes to ours to
load tracks. If we automatically cleared the track history for them every
time they selected a track it would undo any previous work they had done, so
the remove all tracks feature really isn't an option. The TrackHub
suggestion might work, I'll have to talk with our guys, but it seems like a
promising solution. Ideally what we want is something that we can integrate
into our current system.

Thanks,
Brad Davis

[Brooke Rhead]

Hi Brad,

We don't currently have a mechanism in track hubs or in custom tracks to
control visibilities of data hubs, or a way to disconnect from a
particular hub via URL, so on second thought, track hubs might not be
the best solution for now.

Instead, you may be able to get to the custom track table names with the
numbers appended to them by constructing a URL to the Table Browser and
then doing some screen scraping. For instance, this URL will take you
to the Table Browser for hg19 with the Custom Tracks track group selected:

http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=user

You might have to do some experimenting to make it work.

--
Brooke Rhead
UCSC Genome Bioinformatics Group