Question

How to generate a mouse reference genome in STAR?

1

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4.5 years ago

fifty_fifty ▴ 70

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 • 3.5k views

ADD COMMENT • link updated 4.5 years ago by khorms ▴ 230 • written 4.5 years ago by fifty_fifty ▴ 70

score 3 · Accepted Answer · 2020-06-17

3

Entering edit mode

4.5 years ago

khorms ▴ 230

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

ADD COMMENT • link 4.5 years ago by khorms ▴ 230

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

ADD REPLY • link 4.5 years ago by fifty_fifty ▴ 70