Hello David,
We can add this genome to the list to be indexed and added, but for immediate use, simply adding as a custom genome would be the quickest and easiest way to gain access and start using the the genome with tools right now. This also gives you some control over the source: match up the genome source with the GTF file source you plan to use. This can avoid having to rename the chromosome identifiers (they must be an exact match between the two).
Instructions are here for custom genomes: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
And some RNA-seq links, to help with planning the experiment: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results (see 'Tools on the Main server: Example')
Best,
Jen Galaxy team
On 9/25/12 8:11 PM, Stern PhD, David L wrote:
We are considering using Galaxy to map RNA-seq reads to the D. yakuba genome. I notice that this genome is not yet available on the reference genome list. Is there any chance it could be added by the Galaxy team. I suspect you could do it faster and with a higher likelihood of success than I could! Cheers, David
David Stern Group Leader Janelia Farm Research Campus HHMI 19700 Helix Dr. Ashburn, VA 20147
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