<br><font size=2 face="sans-serif">Dear Oliver,</font>
<br>
<br><font size=2 face="sans-serif">Many thanks for your great help. Yes,
It is the type of glyph that I am looking for. Please send me an </font><tt><font size=2>example
of conf.</font></tt>
<br>
<br><tt><font size=2>Thank you again for your great help.</font></tt>
<br>
<br><tt><font size=2>Sincerely</font></tt>
<br>
<br><tt><font size=2>Yinyan</font></tt>
<br>
<br>
<br>
<br>
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<td width=44%><font size=1 face="sans-serif"><b>Oliver Burren <oliver.burren@cimr.cam.ac.uk></b>
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<p><font size=1 face="sans-serif">2010-01-28 11:55</font>
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<div align=right><font size=1 face="sans-serif">To</font></div>
<td><font size=1 face="sans-serif">"Dave Clements, GMOD Help Desk"
<help@gmod.org></font>
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<div align=right><font size=1 face="sans-serif">cc</font></div>
<td><font size=1 face="sans-serif">Yinyan Guo <Yinyan.Guo@dnalandmarks.ca>,
gmod-gbrowse@lists.sourceforge.net</font>
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<div align=right><font size=1 face="sans-serif">Subject</font></div>
<td><font size=1 face="sans-serif">Re: [Gmod-gbrowse] [Gmod-help] How to
put info about "association analysis (p value)" in Gbrowse</font></table>
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<br><tt><font size=2>Dear Yinyan,<br>
<br>
Is this something similar to what you are trying to achieve ?<br>
<br>
http://tinyurl.com/yfzutqa<br>
<br>
If so let me know and I'll be happy to help out by sending example conf
<br>
file etc.<br>
<br>
Thanks,<br>
<br>
Olly Burren<br>
<br>
Dave Clements, GMOD Help Desk wrote:<br>
> Dear Yinyan,<br>
> <br>
> I've cc'd the GBrowse list, which is the best place to post these
discussions.<br>
> <br>
> On Mon, Jan 25, 2010 at 2:07 PM, Yinyan Guo <Yinyan.Guo@dnalandmarks.ca>
wrote:<br>
>> Dear Sir,<br>
>><br>
>> Gbrowse is very good tool to browse genome info (SNP, gene, etc).
Its data<br>
>> structure is simple.<br>
>><br>
>> In association analysis, I have p value for each marker, Is there
any method<br>
>> to put those p value (line) in Bbrowse?<br>
> <br>
> I can think of a couple of ways to do this, depending on your<br>
> situation. If you aren't already using colors (or height or
...) for<br>
> something else, you could set the color of the marker based on its
p<br>
> value. This would be done by putting the p value in column 9
of the<br>
> GFF and using it in a small perl callout routine. You could
also have<br>
> a separate p-value track where you just show p values, again using<br>
> something like color or height. You can also show p-values in
popups<br>
> or link out pages, but then the user has to take some additional<br>
> action to see the information.<br>
> <br>
> I'm not too familiar with association studies. Are the p values<br>
> associated with alleles/variants, or is there at most one p-value
per<br>
> region? If there is only one p-value per region, or if you are
at low<br>
> zoom (zoomed out), you could show the p-values with an xyplot.<br>
> <br>
> Does that help?<br>
> <br>
> Dave C.<br>
>> Thank you in advance for your support.<br>
>><br>
>> Sincerely<br>
>><br>
>> Yinyan<br>
>><br>
> <br>
> <br>
> <br>
<br>
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<br>