Hi
I have been involved in a project related to SNP discovery in plant species. I was wondering if there is any information on trying to use UCSC genome browser for plant genome database, which can be loaded on local galaxy.
Thanks
Viva
Hello,
The main UCSC Genome Browser does not host plant genomes or data as primary assemblies. Perhaps you are using another site with that content? Running a local UCSC Genome Browser and populating it with alternative content is certainly possible.
There is information about the ways of using the browser software at http://genome.ucsc.edu/. Start with the Mirrors, Downloads, and the Help menu (where UCSC can be contacted for Q&A).
A local UCSC Browser and local Galaxy can be configured to interact. Is this what you are trying to do?
Best, Jen, Galaxy team
Hello Jen
This is exactly what I want to know. Thanks for your help. What is the precise meaning of local galaxy and local browser? Can this term can be used for my own galaxy account ?
Regards
Viva
By "local" I mean a Galaxy or UCSC Browser instance that you host yourself (on a laptop, computer, or server). Distinct from any other instances - public, cloud, or anyone else's local. Both Galaxy and UCSC support this. See the UCSC download link for their how-to. See http://getgalaxy.org for Galaxy's how-to.
Glad the other info helped! Jen
