Hi Christopher,
The target "reference genome" can be any fasta file in your history, for
most tools, including mapping tools. However, the assigned "database"
attribute for any datasets that you want to map to this custom reference
would be left as undefined in Galaxy (but this would have no impact on
analysis).
The exception here is if you were running your own instance. For this
case, a native "reference genome" of the modified mm9 genome data could
be loaded. As part of this process, you would be creating the database
attribute "label", all of the indexes, and be able to assign the
database attribute for datasets to this new database label. Instructions
for local installs are in the wiki here: http://getgalaxy.org
To get you started with the filtering, I can let you know that the mm9
database in Galaxy was sourced from UCSC http://genome.ucsc.edu and can
be obtained from their Downloads site.
Hopefully this helps,
Thanks,
Jen
Galaxy team
On 10/13/11 2:33 PM, Christopher Callaway wrote:
I would like to filter out the mm9 mouse build ref genome to only show
MspI sites, and then use that as my “Genome” when uploading my Illumina
data. Anyone have a protocol for that?
Thanks,
Christopher W. Callaway
University of Utah
Dept. of Pediatrics
Division of Neonatology
417 Wakara Way
#2222
Salt Lake City, UT 84108
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--
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http://galaxyproject.org/Support
___________________________________________________________
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:
http://lists.bx.psu.edu/
