[Gmod-ajax] JBrowse Wiggle XY Plot - Positive and negative values for the same coordinate position?

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[Gmod-ajax] JBrowse Wiggle XY Plot - Positive and negative values for the same coordinate position?

Ram Podicheti-2
I am trying to plot the coverage at each base position using Wiggle XY plot on JBrowse. The mapping results from the bam file are exported into a bedgraph and finally to bigwig which I could load into Jbrowse without any issues. 

Now, I would like to plot the coverages on the positive and negative strands separately and there are no issues in this case either as long as I am keeping these data into two separate tracks. Will it be possible to display the coverage on both the strands using a single track, where the density on the positive strand will be a positive number, but that on the negative strand will be a negative number? I tried creating a bedgraph file with both the positive and negative coverage values supplied together, but the "bedgraphToBigWig" program is throwing an error - "Overlapping regions in bedgraph". Any ideas in this regard would be a big help.
Thanks,

Ram

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Re: JBrowse Wiggle XY Plot - Positive and negative values for the same coordinate position?

Robert Buels-2
This isn't possible right now in JBrowse, there is no track type that
can render multiple separate quantitative data sets at the same time on
the same y-axis scale.

It would probably be relatively straightforward to write one, probably
based on the current Wiggle/XYPlot track implementation.  Would you be
interested in working on that Ram?  Initially, you could start
developing the new track type in the context of a JBrowse plugin.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/15/2013 11:22 AM, Podicheti, Ram wrote:

> I am trying to plot the coverage at each base position using Wiggle XY
> plot on JBrowse. The mapping results from the bam file are exported into
> a bedgraph and finally to bigwig which I could load into Jbrowse without
> any issues.
>
> Now, I would like to plot the coverages on the positive and negative
> strands separately and there are no issues in this case either as long
> as I am keeping these data into two separate tracks. Will it be possible
> to display the coverage on both the strands using a single track, where
> the density on the positive strand will be a positive number, but that
> on the negative strand will be a negative number? I tried creating a
> bedgraph file with both the positive and negative coverage values
> supplied together, but the "bedgraphToBigWig" program is throwing an
> error - "Overlapping regions in bedgraph". Any ideas in this regard
> would be a big help.
> Thanks,
>
> Ram
>
>
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> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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>
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>

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Re: JBrowse Wiggle XY Plot - Positive and negative values for the same coordinate position?

Robert Buels-2
Well, I'm on the #gmod channel on Freenode IRC every day during US East
business hours.  Feel free to stop by and I can point you in the right
direction to get started.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/15/2013 07:25 PM, Podicheti, Ram wrote:

> Rob,
> I would love to do that. It is still early days for me with JBrowse, so I might be a little slow.
> Thanks,
>
> Ram
>
> On Jul 15, 2013, at 7:14 PM, Robert Buels wrote:
>
>> This isn't possible right now in JBrowse, there is no track type that can render multiple separate quantitative data sets at the same time on the same y-axis scale.
>>
>> It would probably be relatively straightforward to write one, probably based on the current Wiggle/XYPlot track implementation.  Would you be interested in working on that Ram?  Initially, you could start developing the new track type in the context of a JBrowse plugin.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/15/2013 11:22 AM, Podicheti, Ram wrote:
>>> I am trying to plot the coverage at each base position using Wiggle XY
>>> plot on JBrowse. The mapping results from the bam file are exported into
>>> a bedgraph and finally to bigwig which I could load into Jbrowse without
>>> any issues.
>>>
>>> Now, I would like to plot the coverages on the positive and negative
>>> strands separately and there are no issues in this case either as long
>>> as I am keeping these data into two separate tracks. Will it be possible
>>> to display the coverage on both the strands using a single track, where
>>> the density on the positive strand will be a positive number, but that
>>> on the negative strand will be a negative number? I tried creating a
>>> bedgraph file with both the positive and negative coverage values
>>> supplied together, but the "bedgraphToBigWig" program is throwing an
>>> error - "Overlapping regions in bedgraph". Any ideas in this regard
>>> would be a big help.
>>> Thanks,
>>>
>>> Ram
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> See everything from the browser to the database with AppDynamics
>>> Get end-to-end visibility with application monitoring from AppDynamics
>>> Isolate bottlenecks and diagnose root cause in seconds.
>>> Start your free trial of AppDynamics Pro today!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>
>

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