[galaxy-user] customizing mm9 mouse reference genome and then using that as the ref genome when uploading Illumina data

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