[Gmod-help] Re: Gbrowse question

[Dave Clements]

Hi Brad,

I apologize for the delay in the response.  I've been on holiday for most of
the time since you sent your question, and I've just now got back to your
email.

First, I have not used the Staden or BIOLIGN packages so I'm not sure what
they can and can't do.  I've CC'd this to the help list in case anyone else
has input.

GBrowse can display population genetics data such as genotype and allele
frequencies, and individual genotypes.  The talk you were looking at uses
some custom code to show the frequencies.  I would be happy to send you the
GBrowse config file and some sample data.

However, if I were to do this again, I would probably use the stackedplot
glyph (
http://search.cpan.org/~lds/Bio-Graphics-1.981/lib/Bio/Graphics/Glyph/stackedplot.pm)
or perhaps the HapMap pie or tower glyphs -- take a look at HapMap.org.  (I
meant to redo this data in September using stackedplot - but that now looks
unlikely.)

GBrowse can also show indels, and copy number variation data.  Again, see
HapMap.

However, there are a couple things to think about:
1) GBrowse is very much driven by the concept of a reference sequence.  This
reference does not have to be assembled, but you do need to have something
that is special to tie all your other annotation too.

2) GBrowse shows alignments, but does not calculate the alignments.  GBrowse
also does not support editing.

Please let me know if you have questions.

Thanks,

Dave C.

On Thu, Aug 27, 2009 at 1:12 PM, Bradley Rauh <BRAUH at exchange.clemson.edu>wrote:

>  Hi Dave,
>
> I came across your talk on GBrowse (
> http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf) while trying to figure
> out how to compile Samtools for Staden 2.0 installation (not sure how I got
> there but it was a good thing I think).  Anyway in the talk you have a
> couple slides about using GBrowse for pop gen work.  I am interested in this
> as currently the lab I am in (Dr. Amy Lawton-Rauh at Clemson Univ.) uses
> BioLign and since Tom Hall is no longer supporting this software I have been
> trying to find a suitable replacement.  The problem for us is that we are a
> pop gen lab and are always looking at multiple populations of multiple
> individuals and most sequence alignment programs can’t handle this and still
> edit the sequence.  Am I on the right track with GBrowse?  Is this something
> that may be possible or is Staden 2.0 a better bet?  Thanks for your input.
>
> Cheers,
>
> Brad Rauh
>
>
>
> --
> Dept. Genetics and Biochemistry
> Clemson University
> 102 Jordan Hall
> Clemson, SC 29634
> USA
>
> tel: (864) 656-1507
> fax: (864) 656-6879
> webpage: coming soon
> 'Not all who wander are lost.' - J.R.R. Tolkien
>
>
>



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