Hello, This genome 'Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4)' is currently in the genome builds list as a "database" assignment choice, but the actual genome data is not incorporated into Galaxy (yet). This allows data to be labeled and displayed at the UCSC Genome Browser. As a standard practice, Galaxy includes all UCSC builds, some that we incorporate native data for and some that we do not (but user's can). The genome galGal4 is on the list of genomes to be added to tools on the public main instance as a native genome in the near term. Meanwhile, use the build with tools using the 'custom reference genome' option. Instructions: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Galaxy does not host databases, but UCSC does on their downloads server: http://hgdownload.cse.ucsc.edu/downloads.html Hopefully this helps, Jen Galaxy team On 4/25/12 1:01 PM, Nicholas Beckloff wrote:

Dear Galaxy, I noticed upon uploading a FASTQ file that the ICGSC version of the 2011 November Chicken genome is available. Why is this not available for use with the tools? Also, is this available for download?

-- Nicholas Beckloff, PhD Genomics Core Laboratory Director Department of Genetics and Genome Sciences Case Western Reserve University 2109 Adelbert Road BRB 646 Cleveland, OH 44106 phone: 216-368-2791 fax: 216-368-3432 http://genomics.case.edu email: nmb64@case.edu <mailto:nmb64@case.edu>

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