Hello Joe,
The genome is already included in Galaxy. Click on the pencil icon for a
dataset and search with the term "Staphylococcus" and search through the
entries to locate:
Staphylococcus aureus subsp. aureus str. Newman (18801)
The short label database will be set to "18801". This is how the UCSC
Microbial database content was set up originally and we decided it was
best not to change it.
If you would like help solving issues with annotation files and the
reference genome (native or uploaded, please let us know.
Quick list of things to check:
1 - database short name is same every place it is used (as the assigned
"database" + content within a dataset).
2 - chromosome/contig identifiers are the the same every place they are
used. Even minor differences such as capitalization must be normalized.
3 - data coordinates are with respect to the forward strand and have a
zero-based start (for most formats, as noted in the format specification).
Best,
Jen
Galaxy team
On 10/29/11 7:20 AM, Joe J Harrison wrote:
Hello,
Would you please add Staphylococcus aureus strain Newman to your database?
Workflows to analyze data for genomes available through your database are
really simple - but I must admit that I've been struggling with trying to get
this to work for a genome (and in particular with the annotation) that I've
uploaded myself.
Thanks for the help and the continued support!
Joe
----
Joe J. Harrison
Senior Fellow
Department of Microbiology
University of Washington
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___________________________________________________________
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:
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please use the interface at:
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