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 zoccola@centrescientifique.mc mailto:zoccola@centrescientifique.mc http:// www.centrescientifique.mc http://www.centrescientifique.mc

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