UCSC Genome Browser - question

[Stud. Mona Katharina Tonn,Biomathematik]

Good Morning,

I am working on a project to create overlay plots of our data and therefore I am using the "custom track"-function of the UCSC Genome Browser. During my work a few questions came up.

I found the function "Overlay Method" in the "Graph Configuration Help"-Menu. I think this is a function I need, but it is somehow not activated when I upload two or more custom tracks. Could you explain to me why it is not activated? And when it will be possible to use this function? I also found the alternative to create a multiWig Container and upload a TrackDb-file, but this solution is not working either. Would there be another possibility to create those plots?

I also would like to know whether it is possible to draw a line in my custom tracks, which connects all the points?

Can I make the points bigger than the default value in the "Track Setting"-Menu?

Best regards,

Mona Katharina Tonn

 

[Brooke Rhead]

Hi Mona,

Composite tracks are not supported in the Custom Tracks tool. They are,
however, supported in track hubs:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

Track hubs are a bit more work to set up, but they offer several
advantages over custom tracks: they are easy to share, they support
composite tracks, and all of the data is maintained on your own server,
so it is easy to modify and maintain it.

To create your tracks in a track hub, you will need to use the Hub Track
Database Definition document:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html
specifically, see the multiWig section:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#aggregate

For your questions on the configuration settings in custom tracks, are
you referring to a wiggle type of track? If so, you can find a list of
the settings you can change here:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
You might also want to check for the settings you can change on the Hub
Track Database Definition page mentioned above.

I hope this is helpful. If you have further questions, please contact
us again at gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> --
>
>
>

[Stud. Mona Katharina Tonn,Biomathematik]

Hi,

 

sorry to bother you again. Your information was very helpful, I can now open the URLs on the browser, but when I try to open the URL on the track hub function I get:

 Error TCP non-blocking connect() to .... timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open....

I can not find any solution to this problem. What exactly does that mean?

 

Another thing I am not sure about are the formats. I know what needs to be in a wiggle file, but I am not sure if my conversion .txt to .wig is the right one. How can I convert properly and is a conversion .wig to .bigWig possible on windows?

 

Thanks in advance,

Mona

 

Brooke Rhead <rh...@soe.ucsc.edu> hat am 19. März 2013 um 02:10 geschrieben:
> Hi Mona,
>
> You should still be able to use track hubs with an ftp server that
> requires a password. Construct your bigDataUrls so that they
> incorporate the password as described here:
>
> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE
>
> There are definitely more functions available for track hubs than for
> custom tracks. To get an idea of how track hubs work, hit the "track
> hubs" button under the graphic on the main Genome Browser page
> (http://genome.ucsc.edu/cgi-bin/hgTracks), and go to the "Public Hubs"
> tab to display track hubs contributed by others that have been made
> publicly available. If you see the functionality you need in one of the
> public track hubs, you will know that you will be able to incorporate it
> into your own track hub.
>
> I hope this information is helpful. Please send further questions to

> gen...@soe.ucsc.edu.
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>

> On 3/17/13 6:30 PM, Stud. Mona Katharina Tonn,Biomathematik wrote:
> > Good evening,
> > Thanks for your response.
> > I already tried the track hubs function, but that is not working so far.
> > We have a passwort on our ftp server, could that be a reason?
> > Is it possible to insert wig files instead of bigWig files (we are using
> > Microsoft)?
> > I already found the custom track functions for wiggle files, but for our
> > results we would need the functions I described. So this is then not
> > possible with UCSC?
> > Regards,
> > Mona Katharina Tonn
> >
> > Brooke Rhead <rh...@soe.ucsc.edu> hat am 16. März 2013 um 00:48
> > geschrieben:

[Brooke Rhead]

Hi Mona,

Connection timeout messages could be the result of a number of problems:
an incorrect URL, a firewall, a network outage, etc. The only thing
we can tell from our end is that we are unable to connect to your track
hub. Does the URL that you are supplying to the track hub go to a
hub.txt file such as this one (this is from the "miRcode microRNA sites"
public hub on hg19): http://www.mircode.org/ucscHub/hub.txt ? Is there
a directory hierarchy set up like the example at
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup ?

There is no need to convert a wiggle file that has a .txt extension into
anything else. The wiggle format is a text format. You can change the
extension on the file from .txt to .wig if you like, but either
extension will work for loading a regular custom track (as opposed to a
bigWig or other remote data track) into the Genome Browser.

Instructions for converting wiggle data to bigWig are on our site, here:
http://genome.ucsc.edu/goldenPath/help/bigWig.html

We don't supply any executables for running wigToBigWig on Windows. It
might be possible to run it on Cygwin (http://www.cygwin.com/) on your
Windows machine (I have not tried it here, though!). An easier solution
would be to use the Galaxy website (usegalaxy.org). In the Tools menu
on the left-hand side of the page, select "Convert Formats" and then
"Wig/BedGraph-to-bigWig converter."

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 3/20/13 7:35 AM, Stud. Mona Katharina Tonn,Biomathematik wrote:
> Hi,
> sorry to bother you again. Your information was very helpful, I can now
> open the URLs on the browser, but when I try to open the URL on the
> track hub function I get:

> *Error TCP non-blocking connect() to .... timed-out in select() after
> 10000 milliseconds - Cancelling! Couldn't open....*