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
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: