Questions about GRCm38 Mus_musculus Reference Genome

[seqador]

I downloaded all the files in Ensembl Genome Browser and notice that there are several files with identical names except a couple of letters and I could not figure out the difference or what they mean.

Some files are writen:

Mus_musculus.GRCm38.75.dna.chromosome.X.fa.gz

Mus_musculus.GRCm38.75.dna_sm.chromosome.X.fa.gz

Mus_musculus.GRCm38.75.dna_rm.chromosome.X.fa.gz


I need to index this genome to use an aligner.

Thanks for everybody support.

[GenoMax]

From ftp://ftp.ensembl.org/pub/release-75...lus/dna/README

* 'dna_rm' - masked genomic DNA. Interspersed repeats and low
complexity regions are detected with the RepeatMasker tool and masked
by replacing repeats with 'N's.
* 'dna_sm' - soft-masked genomic DNA. All repeats and low complexity regions
have been replaced with lowercased versions of their nucleic base