Hello Jason,

The short answer is that the database is interpreted from the database assignment of the inputs to the tool.


Have you seen our RNA-seq tutorial? It may answer some of the other questions.
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Best,

Jen
Galaxy team

On 6/26/12 2:02 PM, Jason Serviss wrote:
Hello Jennifer,

Thank you for your prompt reply! Yes, I am using the public main
Galaxy at the link you included. So just to clarify (sorry its my
first time doing this), if I select "locally cached" the analysis will
automatically be done with a Sequence Data file located on the server?
How is the proper species Sequence Data selected (i.e. h19 in this
case) and the version? I didn't receive a prompt to select any
specific database after clicking the "locally cached" option. Do I
need to place h19 in my history? I looked in Galaxy for a link to
"Cuff*RNA-seq tools (which you had mentioned), but couldn't manage to
locate it... Thanks for your patience!

Kind Regards,
Jason

2012/6/26, Jennifer Jackson <j...@bx.psu.edu>:
Hello Jason,

Are you using the public main Galaxy instance at
http://main.g2.bx.psu.edu (usegalaxy.org)? The hg19 database can be used
as a "locally cached" reference genome with the Cuff* RNA-seq tools, so
there isn't any need to load external fasta files. If you do decide to
use a custom genome in the future (a different genome), individual
chromosomes can be merged with the tool "Text Manipulation ->
Concatenate datasets".

More help with format is on our wiki:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

Thanks,

Jen
Galaxy team

On 6/26/12 8:50 AM, Jason Serviss wrote:
Hi!

Just a quick question.... I am trying to use cuffcompare for human
data and want to use a Sequence Data (h19). I can only seem to find
the fasta files divided by chromosome. If I upload all of these files
individually will the program be able to simultaneously use the files
(it looks as though there is only space to input 1 file...)? Or do I
need to find the whole genome in 1 Sequence Data file? Thanks in
advance for your help!


Kind Regards,
Jason
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--
Jennifer Jackson
http://galaxyproject.org





--
Jennifer Jackson
http://galaxyproject.org



___________________________________________________________
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:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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 http://lists.bx.psu.edu/

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