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
Jen Galaxy team
On 6/26/12 2:02 PM, Jason Serviss wrote:
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 firstname.lastname@example.org:
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
Jen Galaxy team
On 6/26/12 8:50 AM, Jason Serviss wrote:
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 ___________________________________________________________ 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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