I am planning to use STAR to map am RNA-seq I have to a mouse genome. I have never done that before. According to the [manual][1], I need to give a path to fasta files. When I looked into [Ensembl][2] database, I found several fasta files for different chromosomes. 

I would appreciate any opinion, advice, or link on how to choose fasta files for mouse.

Thank you!


  [1]: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
  [2]: ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/
In the Ensembl link you attached, there are files that are named something-something-"assembly", for example Mus_musculus.GRCm38.dna.primary_assembly - that is what you need