Question: Installing standalone Galaxy with reference geneome
gravatar for simplitia
4.6 years ago by
United States
simplitia0 wrote:

Dear all, newbie question here. 

So I installed Galaxy on my linux box.  When I try to upload a dataset I see a drop down for reference genome; I chose this and was able to upload successfully.  However, when I tried to use a tool that I installed, TopHat Illumina, the place where the choose reference genome does not contain any of the genome listed in the upload section. Its just an empty box.  Question I have is how do I install a reference genome (ie mouse mm9) so that I can get it to work with TopHat.  I'm a bit confused since it was present in the upload section but not here, so maybe I don't need to install the reference genome?  


thank you very much!


ADD COMMENTlink modified 4.6 years ago by Dannon Baker3.7k • written 4.6 years ago by simplitia0
gravatar for Dannon Baker
4.6 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

You do need to install reference genomes on your own.  As they can be very large, we don't ship them with Galaxy.  See for more details.

Hope this helps!


ADD COMMENTlink written 4.6 years ago by Dannon Baker3.7k

Thanks Dannon: I will check this out.  I even found compile index files for Bowtie link below in case someone else needs it.

ADD REPLYlink written 4.6 years ago by simplitia0
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