[Feedback] [Website feedback] SSR and older markers

[Marcela K. Monaco]

Hi Aaron,

Not sure if anybody else responded to your query earlier.  If not, sorry I
just noticed this while purging our feedback list.

The problem with our current SSRs is that most have not been remapped to
the latest assemblies, so they couldn't be simply uploaded to the genome
browser.  Lifting coordinates of something not as precise as gene locations
(e.g., QTLs and certain markers) is tricky and would need to be
post-processed / hand curated to see the rough region where for example,
the big QTLs map, i.e. the start and end position without outliers.

Marcela

==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851


On Fri, Feb 28, 2014 at 10:39 AM, aaron.jackson at ars.usda.gov <
aaron.jackson at ars.usda.gov> wrote:

> Aaron Jackson (aaron.jackson at ars.usda.gov) sent a message using the
> contact
> form at http://www.gramene.org/contact.
>
> Hello,
> For many years Gramene listed SSR markers and older markers (such as
> RFLP's)
> on the "region in detail" page of ensemble.  I am glad to see that AFFY
> markers and other SNP markers have been added but I no longer see SSR
> markers
> as an option for display.  Is there a way this feature can be added back
> on?
> Our lab, as well as many breeders still routinely use SSR markers.  There
> has
> also been a lot of literature published on SSR markers which still makes
> them
> a valuable tool for identifying regions of interest.  Labs that do not
> actively run SSR markers can still use  this information as anchor
> positions
> for further identifying regions of interest and mapping projects.
> Thanks,
> Aaron
>
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