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!
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