[Gmod-help] Re: [Gmod-gbrowse] Presentation of data in Gbrowse

[ankita narang]

Hi Dave ,

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.

Regards
Ankita

On Fri, Jun 12, 2009 at 8:14 AM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Ankita,
>
> A couple of thoughts on your questions.  Have you looked at the HapMap
> project data at all?  I'm guessing you have based on your reference to
> pie charts.  HapMap also has an allele bars glyph that might scale
> better to 26 populations.  Unfortunately, I'm not sure what the
> release status of those glyphs is.
>
> If your populations have geographic centers associated with them then
> you can use the work described in the (just uploaded today)
> presentation: http://gmod.org/wiki/Image:CMapGBrowseSMBE2009.pdf.
> This shows you pie graphs on a map.
>
> If you want to have each population's frequency info in a separate
> track (although that would mean 52 tracks just for frequency data, you
> could use the approach used with the threespine stickleback data in
> the (also just uploaded today) presentation at
> http://gmod.org/wiki/Image:GMODGBrowseSMBE2009.pdf.  Depending upon
> your volume of data, that approach may or may not scale up to your
> needs.  The technology behind this is not explained in the
> presentation.  If this looks interesting we can talk more.
>
> Finally, the stackedplot glyph
> (
> http://search.cpan.org/~lds/Bio-Graphics/lib/Bio/Graphics/Glyph/stackedplot.pm<http://search.cpan.org/%7Elds/Bio-Graphics/lib/Bio/Graphics/Glyph/stackedplot.pm>
> )
> is another way to show data like this. I haven't used it myself, but
> the description and the png created by the example code make it look
> promising.  In fact, I might redo the work in the presentation to use
> the stackedplot glyph.
>
> Cheers,
>
> Dave C.
>
> On Thu, Jun 11, 2009 at 6:26 AM, ankita narang
> <ankita.bioinfo77 at gmail.com> wrote:
> >
> > Hi Sheldon,
> > 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.
> >
> > Regards
> > Ankita.
> >
> >
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