[Gmod-ajax] Displaying Quantitative Data Using Multiple Colors on JBrowse

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[Gmod-ajax] Displaying Quantitative Data Using Multiple Colors on JBrowse

Murali Podicheti
I am trying to display methylation data on jbrowse with the height of each peak representing the percent of methylation. My current approach is a wiggle/XYPlot reflecting data from a bigwig file. I am wondering if it would be possible to show each methylation site with a different color based on the type of methylation such as CG, CHG or CHH. One option I have currently is to keep these three types of data separate and post them on three different tracks. But it would be more intuitive if I can keep them all on a single track and color coded. I don’t think it is possible with Wiggle/XYPlot. Is there some other method that I could use? Any ideas?

Ram
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Re: Displaying Quantitative Data Using Multiple Colors on JBrowse

Colin
I don't have any good answer for jbrowse but this feature appears to have been added to the UCSC browser http://genome.ucsc.edu/goldenPath/newsarch.html#2014

There are 'combination' tracks for bigwig files in jbrowse, and perhaps this could be a starting point.

-Colin


On Sun, Apr 13, 2014 at 11:17 AM, Murali Podicheti <[hidden email]> wrote:
I am trying to display methylation data on jbrowse with the height of each peak representing the percent of methylation. My current approach is a wiggle/XYPlot reflecting data from a bigwig file. I am wondering if it would be possible to show each methylation site with a different color based on the type of methylation such as CG, CHG or CHH. One option I have currently is to keep these three types of data separate and post them on three different tracks. But it would be more intuitive if I can keep them all on a single track and color coded. I don’t think it is possible with Wiggle/XYPlot. Is there some other method that I could use? Any ideas?

Ram
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Re: Displaying Quantitative Data Using Multiple Colors on JBrowse

vkrishna
In reply to this post by Murali Podicheti
Hi Ram,

You can refer to the JBrowse implementation made for the EPIC-CoGe project (http://genomevolution.org/wiki/index.php/EPIC-CoGe) where they deal with large number of methylation datasets. They have created a new glyph called Wiggle/MultiXYPlot.

They have a github organization page: https://github.com/LyonsLab which probably has the code as well.

Hope this helps!

Best,
Vivek

On Apr 13, 2014, at 12:17 PM, Murali Podicheti <[hidden email]> wrote:

I am trying to display methylation data on jbrowse with the height of each peak representing the percent of methylation. My current approach is a wiggle/XYPlot reflecting data from a bigwig file. I am wondering if it would be possible to show each methylation site with a different color based on the type of methylation such as CG, CHG or CHH. One option I have currently is to keep these three types of data separate and post them on three different tracks. But it would be more intuitive if I can keep them all on a single track and color coded. I don’t think it is possible with Wiggle/XYPlot. Is there some other method that I could use? Any ideas?

Ram
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Re: Displaying Quantitative Data Using Multiple Colors on JBrowse

Colin
Thanks Vivek, I did not know about that! Very cool feature. We will have to see if we can talk to them about that implementation.

-Colin


On Thu, May 8, 2014 at 8:38 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Ram,

You can refer to the JBrowse implementation made for the EPIC-CoGe project (http://genomevolution.org/wiki/index.php/EPIC-CoGe) where they deal with large number of methylation datasets. They have created a new glyph called Wiggle/MultiXYPlot.

They have a github organization page: https://github.com/LyonsLab which probably has the code as well.

Hope this helps!

Best,
Vivek

On Apr 13, 2014, at 12:17 PM, Murali Podicheti <[hidden email]> wrote:

I am trying to display methylation data on jbrowse with the height of each peak representing the percent of methylation. My current approach is a wiggle/XYPlot reflecting data from a bigwig file. I am wondering if it would be possible to show each methylation site with a different color based on the type of methylation such as CG, CHG or CHH. One option I have currently is to keep these three types of data separate and post them on three different tracks. But it would be more intuitive if I can keep them all on a single track and color coded. I don’t think it is possible with Wiggle/XYPlot. Is there some other method that I could use? Any ideas?

Ram
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