The UCSC utility twoBitToFa can get the sequence for an individual chromosome at a time via the -seq option, which you can run in a loop for each chromosome:

$ wget  http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.chrom.sizes
$ for chr in $(cut -f1 rn6.chrom.sizes); do twoBitToFa -seq="${chr}" http://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.2bit $chr.fa; done
$ # verify with the faSize util:
$ head -1 rn6.chrom.sizes
chr1    282763074
$ faSize chr1.fa
282763074 bases (14711797 N's 268051277 real 153502700 upper 114548577 lower) in 1 sequences in 1 files
%40.51 masked total, %42.73 masked real

You can download twoBitToFa and faSize from the following the directory appropriate for your operating system here: http://hgdownload.soe.ucsc.edu/admin/exe/

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: genome@soe.ucsc.edu
• Questions involving private data: genome-www@soe.ucsc.edu
• Questions involving mirror sites: genome-mirror@ose.ucsc.edu

ChrisL from the UCSC Genome Browser

FYI, NCBI Rno6 chromosome wise sequences are available at: ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ and ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/Assembled_chromosomes/seq/

download from http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz and split by file: e.g: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File