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: nm...@case.edu <mailto:nm...@case.edu>



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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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