[Gmod-help] [hapmap.org #5081] Re: [Gmod-gbrowse] Presentation of data in Gbrowse

[Marcela K Tello-Ruiz via RT]

Hi Dave, Ankita,

The allele_column_multi.pm we use to represent the 11 hapmap3
populations is available for download from
http://ftp.hapmap.org/gbrowse/2009-01_phaseIII/glyph/

Best,

Marcela


> [help at gmod.org - Thu Jun 11 22:46:02 2009]:
> 
> 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)
> 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.
> >
> >
>   
------------------------------------------------------------------------------
> > Crystal Reports - New Free Runtime and 30 Day Trial
> > Check out the new simplified licensing option that enables unlimited
> > royalty-free distribution of the report engine for externally facing
> > server and web deployment.
> > http://p.sf.net/sfu/businessobjects
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> 
> 
> --
> Was this helpful?  Let us know at
>    http://gmod.org/wiki/Help_Desk_Feedback
> 
> Learn more about GMOD at:
>  AGA Next Gen Seq in Non-Models:
>    http://www.regonline.com/Nextgeneration
>  Galaxy Workshop at NBIC: http://www.nbic.nl/nbic/newsevents/Galaxy/
> 
> 
> 
-- 
Marcela K. Tello-Ruiz
HapMap Data Coordination Center
Cold Spring Harbor Laboratory