Hi David,

For NGS data, the tools under "NGS: Indel Analysis" can build simple BED files of indels from SAM files that can be viewed in Galaxy (Visualization tab - i.e. Trackster). For viral genomes, you will not be able to use UCSC. The Galaxy 101 tutorial includes some basic SNP analysis and visualization tasks that may help you to orient:
http://main.g2.bx.psu.edu/u/aun1/p/galaxy101

You may get some more replies, but to pull up old responses on the galaxy-user and galaxy-dev mailing list, the archives are here:

http://lists.bx.psu.edu/pipermail/galaxy-user/
http://lists.bx.psu.edu/pipermail/galaxy-dev/

To search, use google and enter:

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

plus enter whatever keywords would identify your questions (perhaps your name?)

Other list members are encouraged to reply to David's inquiry with more help again,

Best!

Jen
Galaxy team


On 5/3/11 10:03 AM, David Matthews wrote:
Hi,

I recently sent out an email asking if anyone knew much about analysis
of SNPs etc and how to visualise them. I got some very useful answers
and planned to return to the problem when I got a better chance to work
on this in some depth. I now have the time but, like an idiot, I've
accidentally deleted those email replies! So can I please ask again,
does anyone have experience of SNP analysis and, especially,
visualisation that can hold my hand whilst I work this out (apologies to
the ones who replied last time but can you get in touch again !)?


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk <mailto:d.a.matth...@bristol.ac.uk>






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