Hello Oliver,

You can compare SNP datasets using the tools under "RGENETICS" and "Human Genome Variation". dbSNP and 1000 Genomes data are locally cashed in our Libraries, making them easy to load into a history and use.


Also, here is an example workflow that includes sample SNP analysis (dbSNP vs 1000 genomes):
http://main.g2.bx.psu.edu/u/ericy/p/chry-1000-genomes

Hopefully this helps,

Best,

Jen
Galaxy team


On 5/9/11 8:05 AM, Oliver, Gavin wrote:
Hi,

I am new to Galaxy and am wondering what tools are available for
annotation of SNPs?

I know that snpEff is implemented in Galaxy and this enables annotation
such as location and predicted effect, however I am wondering if there
are any automated means of annotating a polymorphism as known/novel or
determining its frequency in the population.

Does Galaxy offer anything like this or would it be necessary to create
scripts that would for exampole compare to dbSNP for uniqueness and the
1000 genomes project for frequency.

Best,

Gavin

****

**The contents of this message and any attachments to it are
confidential and may be legally privileged. If you have received this
message in error, you should delete it from your system immediately and
advise the sender.**

****

**Almac Group (UK) Limited, registered no. NI061368.Almac Sciences
Limited, registered no. NI041550.Almac Discovery Limited, registered no.
NI046249. Almac Pharma Services Limited, registered no. NI045055.Almac
Clinical Services Limited, registered no. NI041905.Almac Clinical
Technologies Limited, registered no. NI061202. Almac Diagnostics
Limited, registered no. NI043067.All preceding companies are registered
in Northern Ireland with a registered office address of Almac House, 20
Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. **

****

**Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. **

****

**Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac
Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are
Delaware limited liability companies and Almac Group Incorporated is a
Delaware Corporation. More information on the Almac Group can be found
on the Almac website: www.almacgroup.com <http://www.almacgroup.com>**

****



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to