Re: [gmod-cmap] Representation of Physical Map assignments?

[Ben F. <fag...@gm...>]

Hi John,

I don't know if this is the most elegant solution but for markers and
such that are only assigned to a chromosome, I might create them as
features that span the full length of the chromosome.

Then, you can either use a spanning glyph like "span" or "i_beam" to
show the size. Or you can reduce the clutter by using a smaller glyph
like "right_facing_arrow" which will simply be placed in the middle of
feature.

The advantage of making a giant feature is that it will always be
displayed even when you are zoomed in.

Additionally, you could create separate feature types for those markers
to further differentiate them from the others.  (You will also want to
add them to the "add_name_correspondence" option in the config file.)

Hopefully this helps.  Sorry about the delay.  Let me know if you have
any other questions.

Ben

On Fri, 2008-08-08 at 12:10 +1200, John McCallum wrote:
> Hi
> I am interested in any suggestions or pointers to elegant implemented
> solutions in peoples CMAPs for the following:
> 
> In Allium we are at a rather primitive stage in proceedings and we have
> many markers and phenotypes that have been assigned to physical
> chromosomes using alien addition lines but not mapped. In  a number of
> cases we have markers mapped in one species but only chromosomally
> assigned in another and vice versa.
> These are quite important to us and I would like to represent these
> somehow so that in addition to viewing a linkage group one  could see
> markers assigned to the corresponding chromosome.
> 
> Any suggestions?
> 
> Regards
> John
> 
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
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> 
> Visit our website at http://www.crop.cri.nz 
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