RNor_6.0 was released recently
http://www.ncbi.nlm.nih.gov/assembly/GCA_000001895.4/#/def
Is it possible to add this assembly to the main Galaxy server?
And, in addition, is it possible to add to Main Galaxy server RNA-seq mapper STAR?
The author of mapper, Alex Dobbin, gave permission for such an action... (http://seqanswers.com/forums/showthread.php?t=27470&highlight=star&page=5)
Hello,
When UCSC incorporates a new genome that they normally support, it is our usual trigger to also incorporate it. This aids greatly with reference annotation and such staying in sync over time. I do not see a new browser started yet for this genomes on their test server, but this is still new.
If for some reason UCSC would choose not to include it, at that time we would consider adding it directly from NCBI (or Ensembl). In short, the logic is to add the the best genome release that is a fit for available annotation, starting with the source originally used (source for prior included builds).
For the STAR tool, we have chosen so far to support the Tuxedo pipeline for RNA-seq analysis on the public Main Galaxy instance at http://usegalaxy.org. You can open a request that this tool be included as well, and our team will review/prioritize. Use Trello for this - help is here in our wiki:
https://wiki.galaxyproject.org/Issues
Take care, Jen, Galaxy team
And is it possible now to add to Main Galaxy as system-installed the build of RNor_6.0 assembly of rat genome???
It is now available on UCSC....
http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=472600999_8CiAuj8o6cQzEC4oD3TYLwvrSOY8&clade=mammal&org=Rat&db=rn6
This genome will be included in the next data update. Track progress here: https://github.com/galaxyproject/galaxy/issues/1470
Thanks, Jen
