Displaying transcription tiling array data in gbrowse

[vipin.ts]

I would like to display the transcription tiling array data for different set of experiments.

I used a configuration track as follows.

[TilingArray]
feature      = affy
glyph        = graded_segments
fgcolor      = black
bgcolor      = \&score_color
height       = 15
category     = Expression Tracks
description  = 0
label        = 0
connector    = disable
key          = Tiling array

When I uploaded multiple experiment data, I am unable to show each track of display for each experiment.
It will be good if you can suggest me a way that I can display each experiment in each track.

Thanks in advance
--
Vipin T S
Friedrich Miescher Laboratory of the Max Planck Society
Spemannstrasse 39, 72076
Tuebingen, Germany
Tel:[phone]


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[Scott Cain-4]

Hello Vipin,

If you use a different source (the text in the second column) for each  
experiment, you can specify different track definitions for each  
feature and source combination.  So if you have two different sources,  
test1 and test2, you could specify two different track definitions  
that use:

feature = affy:test1

and

feature = affy:test2

Scott


On Sep 16, 2009, at 9:40 AM, Vipin TS wrote:

> I would like to display the transcription tiling array data for  
> different set of experiments.
>
> I used a configuration track as follows.
>
> [TilingArray]
> feature      = affy
> glyph        = graded_segments
> fgcolor      = black
> bgcolor      = \&score_color
> height       = 15
> category     = Expression Tracks
> description  = 0
> label        = 0
> connector    = disable
> key          = Tiling array
>
> When I uploaded multiple experiment data, I am unable to show each  
> track of display for each experiment.
> It will be good if you can suggest me a way that I can display each  
> experiment in each track.
>
> Thanks in advance
> --
> Vipin T S
> Friedrich Miescher Laboratory of the Max Planck Society
> Spemannstrasse 39, 72076
> Tuebingen, Germany
> Tel:[phone]
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9-12, 2009. Register  
> now!
> http://p.sf.net/sfu/devconf_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





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[Scott Cain-4]

Hi Vipin,

Please keep your responses on the mailing list.

Try setting the "bump density" option equal to 0 or 1, which should
make them always collapse to the same line.  See:

  http://gmod.org/wiki/CONFIGURE_HOWTO#Track_Sections

When you do that, you may want to try setting the fgcolor equal to the
bgcolor, otherwise there may be too many black lines between the
features.  Of course, that is up to you; it is a aesthetic decision.

Scott


On Wed, Sep 16, 2009 at 11:37 AM, Vipin TS <vipin.ts@...> wrote:

> Hi Scott,
>
> Also I have one more doubt. Please find the attached file with this mail. It
> is a screen shot for my gbrowse display.
> Here you can see that each tiling array experiment result are spread in
> multiple lines. I would like to show all the segments in a single line. Can
> please help me on the same. Would that be possible?
>
> Thanks in advance,
> Vipin T S
>
> 2009/9/16 Scott Cain <scott@...>
>>
>> Hello Vipin,
>>
>> If you use a different source (the text in the second column) for each
>> experiment, you can specify different track definitions for each feature and
>> source combination.  So if you have two different sources, test1 and test2,
>> you could specify two different track definitions that use:
>>
>> feature = affy:test1
>>
>> and
>>
>> feature = affy:test2
>>
>> Scott
>>
>>
>> On Sep 16, 2009, at 9:40 AM, Vipin TS wrote:
>>
>>> I would like to display the transcription tiling array data for different
>>> set of experiments.
>>>
>>> I used a configuration track as follows.
>>>
>>> [TilingArray]
>>> feature      = affy
>>> glyph        = graded_segments
>>> fgcolor      = black
>>> bgcolor      = \&score_color
>>> height       = 15
>>> category     = Expression Tracks
>>> description  = 0
>>> label        = 0
>>> connector    = disable
>>> key          = Tiling array
>>>
>>> When I uploaded multiple experiment data, I am unable to show each track
>>> of display for each experiment.
>>> It will be good if you can suggest me a way that I can display each
>>> experiment in each track.
>>>
>>> Thanks in advance
>>> --
>>> Vipin T S
>>> Friedrich Miescher Laboratory of the Max Planck Society
>>> Spemannstrasse 39, 72076
>>> Tuebingen, Germany
>>> Tel:[phone]
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Come build with us! The BlackBerry® Developer Conference in SF, CA
>>> is the only developer event you need to attend this year. Jumpstart your
>>> developing skills, take BlackBerry mobile applications to market and stay
>>> ahead of the curve. Join us from November 9-12, 2009. Register
>>> now!
>>>
>>> http://p.sf.net/sfu/devconf_______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> -----------------------------------------------------------------------
>> Scott Cain, Ph. D. scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>>
>>
>
>
>
> --
> Vipin T S
> Friedrich Miescher Laboratory of the Max Planck Society
> Spemannstrasse 39, 72076
> Tuebingen, Germany
> Tel:[phone]
> Mobile: [phone]
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9-12, 2009. Register now!
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