Hi Dave ,<br><br>I have seen their data , but they have 7 populations at present , their glyphs are also available , I am reading about NexGen sequencing from Past 2 days , Thanks for updating me for tutorials. I will go through them and mail you again.<br>
<br>Regards<br>Ankita<br><br><div class="gmail_quote">On Fri, Jun 12, 2009 at 8:14 AM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Ankita,<br>
<br>
A couple of thoughts on your questions. Have you looked at the HapMap<br>
project data at all? I'm guessing you have based on your reference to<br>
pie charts. HapMap also has an allele bars glyph that might scale<br>
better to 26 populations. Unfortunately, I'm not sure what the<br>
release status of those glyphs is.<br>
<br>
If your populations have geographic centers associated with them then<br>
you can use the work described in the (just uploaded today)<br>
presentation: <a href="http://gmod.org/wiki/Image:CMapGBrowseSMBE2009.pdf" target="_blank">http://gmod.org/wiki/Image:CMapGBrowseSMBE2009.pdf</a>.<br>
This shows you pie graphs on a map.<br>
<br>
If you want to have each population's frequency info in a separate<br>
track (although that would mean 52 tracks just for frequency data, you<br>
could use the approach used with the threespine stickleback data in<br>
the (also just uploaded today) presentation at<br>
<a href="http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf" target="_blank">http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf</a>. Depending upon<br>
your volume of data, that approach may or may not scale up to your<br>
needs. The technology behind this is not explained in the<br>
presentation. If this looks interesting we can talk more.<br>
<br>
Finally, the stackedplot glyph<br>
(<a href="http://search.cpan.org/%7Elds/Bio-Graphics/lib/Bio/Graphics/Glyph/stackedplot.pm" target="_blank">http://search.cpan.org/~lds/Bio-Graphics/lib/Bio/Graphics/Glyph/stackedplot.pm</a>)<br>
is another way to show data like this. I haven't used it myself, but<br>
the description and the png created by the example code make it look<br>
promising. In fact, I might redo the work in the presentation to use<br>
the stackedplot glyph.<br>
<br>
Cheers,<br>
<br>
Dave C.<br>
<div><div></div><div class="h5"><br>
On Thu, Jun 11, 2009 at 6:26 AM, ankita narang<br>
<<a href="mailto:ankita.bioinfo77@gmail.com">ankita.bioinfo77@gmail.com</a>> wrote:<br>
><br>
> Hi Sheldon,<br>
> I have query regarding GBrowse , I have Affy 50k SNP data for 26 populations , i have minor-allele , genotype and their corresponding frequency information ,i can present snp and its minor-allele and genotype allele in track but to represent their frequency information for 26 populations , If i dumped in differrent database and use this information through plugin is not a good idea i think , to make piechart , xyplot what can be better idea i am not getting. Please suggest what could be the most effective way to present the informative data .Do NexGen Sequencing have some module for such data.<br>
><br>
> Regards<br>
> Ankita.<br>
><br>
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