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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