Hello Didier,

A custom reference genome can be used with the RNA-seq tools. In short, you load a fasta file (your custom reference genome) using FTP to the public Galaxy server, then select it for use with the tools (genome "from the history"). Help is in our wiki:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

Please let us know if you more information,

Jen
Galaxy team

On 10/18/12 11:13 PM, Didier Zoccola wrote:
Hi everyone,

I am Didier Zoccola and i am marine biologist working on corals.  I
would like to do a illumina mapping from RNA-seq coming from
environmental conditions. For that, i would like to use Bowtie but i
have not a reference genome. We have done a /de novo/ transcriptome
using trinity assembly. I have filter by quality all my data. One
possible thing is to download all the manipulated sequences on my
computer and use  Bowtie on my machine but it will take long time
because my computer is not appropriate for this. An other thing is to
download my reference transcriptome on your server. Is it possible?

If not, what is the characteristics of the "ideal" computer to do the
job locally ?

thank you in advance

Best regards


Didier Zoccola
------------------------------------------
Centre Scientifique de Monaco
avenue Saint Martin
98000 Monaco
☎ +377 97 77 08 73
zocc...@centrescientifique.mc <mailto:zocc...@centrescientifique.mc>
http:// www.centrescientifique.mc <http://www.centrescientifique.mc>






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