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How to generate a mouse reference genome in STAR?

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, I need to give a path to fasta files. When I looked into Ensembl 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!

genome alignment mouse rna-seq star
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updated by khorms khorms • written by fifty_fifty • fifty_fifty

1 answer

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

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written by khorms khorms

Thank you! The manual said to include certain chromosomes that is why I got confused

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written by fifty_fifty • fifty_fifty

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