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?
Christopher W. Callaway
University of Utah
Dept. of Pediatrics
Division of Neonatology
417 Wakara Way
Salt Lake City, UT 84108
The target "reference genome" can be any fasta file in your history,
most tools, including mapping tools. However, the assigned "database"
attribute for any datasets that you want to map to this custom
would be left as undefined in Galaxy (but this would have no impact on
The exception here is if you were running your own instance. For this
case, a native "reference genome" of the modified mm9 genome data
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.
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
be obtained from their Downloads site.
Hopefully this helps,