RNA-seq with Staphylococcus aureus strain Newman

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RNA-seq with Staphylococcus aureus strain Newman

Joe Harrison
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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Re: RNA-seq with Staphylococcus aureus strain Newman

Jen Hillman-Jackson
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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org