Question: RNor_6.0 assembly of rat genome - to add it to Galaxy
0
gravatar for sulamora
4.3 years ago by
sulamora0
Russian Federation
sulamora0 wrote:

RNor_6.0 was released recently

http://www.ncbi.nlm.nih.gov/assembly/GCA_000001895.4/#/def

ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Rattus_norvegicus/Rnor_6.0/

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)

assembly alignment • 1.6k views
ADD COMMENTlink modified 2.4 years ago by gupta30 • written 4.3 years ago by sulamora0
1
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

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

 

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by sulamora0
1

This genome will be included in the next data update. Track progress here: https://github.com/galaxyproject/galaxy/issues/1470

Thanks, Jen

ADD REPLYlink written 2.7 years ago by Jennifer Hillman Jackson25k
0
gravatar for gupta
2.4 years ago by
gupta30
gupta30 wrote:

Hello,

For the option: Get data --> Upload file from your computer

I still do not see 'RNor_6.0' in the options for Genome. Has this not yet been updated?

Thanks. Best wishes, PG

ADD COMMENTlink written 2.4 years ago by gupta30
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