Question: How to generate a mouse reference genome in STAR?
1
gravatar for biostarukha
19 days ago by
biostarukha10
biostarukha10 wrote:

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!

ADD COMMENTlink modified 19 days ago by khorms110 • written 19 days ago by biostarukha10
2
gravatar for khorms
19 days ago by
khorms110
Moscow
khorms110 wrote:

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 COMMENTlink written 19 days ago by khorms110

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

ADD REPLYlink written 19 days ago by biostarukha10
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