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