Trackster set display mode - Output looks all the same

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Trackster set display mode - Output looks all the same

Linda Cham

Hi.

Running Galaxy stable_2013.06.03 version on RH6.2 with postgresl db.
Generated bam and vcf file to view under Trackster.

Set up trackster by following http://wiki.galaxyproject.org/Learn/Visualization directions.

No matter what I choose for "Set display mode",  all I see is blocks of color for the vcf (is that the INTENSITY mode?)  and a line for the BAM file which doesn't seem to be what the directions above for the Histogram, Line, Filled, and Intensity are supposed to look like.

Not sure what the output supposed to look like so can't tell if it is correct or not.

1- Should the "Set display mode" give out different output?
2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect?  Might there be some trackster setup that I might be missing for it to draw incorrectly?



What is shown:



Not sure if the 2 images that I had inserted above will be viewable after I send out the request.

Thanks in advance.

Linda
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Re: Trackster set display mode - Output looks all the same

Jeremy Goecks
Hi Linda,

1- Should the "Set display mode" give out different output?

Not yet. 

VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted.

If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example.



2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect?  Might there be some trackster setup that I might be missing for it to draw incorrectly?

Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page:

<a href="http://wiki.galaxyproject.org/Visualization Setup">http://wiki.galaxyproject.org/Visualization%20Setup

Best,
J.

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Re: Trackster set display mode - Output looks all the same

Linda Cham

Thank you Jeremy.
The new wiki page looks great!

Regards,
Linda


Inactive hide details for Jeremy Goecks ---06/11/2013 12:56:53 PM---Hi Linda, > 1- Should the "Set display mode" give out diffeJeremy Goecks ---06/11/2013 12:56:53 PM---Hi Linda, > 1- Should the "Set display mode" give out different output?

From: Jeremy Goecks <[hidden email]>
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: <[hidden email]>
Date: 06/11/2013 12:56 PM
Subject: Re: [galaxy-dev] Trackster set display mode - Output looks all the same





Hi Linda,

    1- Should the "Set display mode" give out different output?

Not yet.

VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted.

If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example.




    2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect?  Might there be some trackster setup that I might be missing for it to draw incorrectly?

Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page:

http://wiki.galaxyproject.org/Visualization%20Setup

Best,
J.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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