Hello Matt, If you are using the public Main Galaxy instance or a Cloud Galaxy AMI, the genome should be available. But on a local instance, reference genomes need to be set up. These are the instructions: http://wiki.galaxyproject.org/Admin/Data%20Integration http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#May_29th_2013_FTP_lo... If you are on a local, you will probably want to start asking questions about local set-up on the galaxy-dev@bx.psu.edu mailing list and also consider subscribing/following it. http://wiki.galaxyproject.org/Support#Mailing_Lists Take care, Jen Galaxy team On 7/29/13 10:51 AM, Matthew Girgenti wrote:

Hi I'm currently using the Galaxy pipeline to analyze my illumina chip-seq data. When I try to use "NGA: Mapping>Map with Bowtie for Illumina" to map my reads there is no rat reference genome. I says I should contact galaxy. Should I simply upload the genome to proceed with analysis? Thanks Matt ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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