RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, which reference genome should I download when using STAR aligner?

Question

[FantasticAI]

I'm trying to perform alignment using STAR for my RNA-Seq data of Lung, right ventricle (RV) and left ventricle (LV) of Mouse, I wonder which reference genome should I use? Sorry for such silly question, I don't have relative experience before. Based on my research, I think Mus musculus (assembly GRCm39) could be a better choice? Is there any other better options?

Answer 1

[GenoMax]

You can use GRCm39. Download the genome and GTF from GENCODE. You will want the primary assembly and corresponding GTF.

[FantasticAI]

Thank you for the quick response, I wonder if the two data files you provided above is the same files as the the ones on Ensembl?

"Mus_musculus.GRCm39.104.gtf.gz" and "Mus_musculus.GRCm39.dna_sm.primary_assembly.fa.gz"

I guess they are same, just different names, right? which one would you prefer to use in practice?

[FantasticAI]

I found my answer in the STAR manual, basically GENCODE is strong recommended for human and mouse. Thank you