Hello, this is a very basic question but I was wondering if someone could help me understand if I've used the correct GTF file and Fasta file for the mouse genome indexing. I got the relevant Fasta file and GTF file from ensembl: GTF:ftp.ensembl.org/pub/release-103/gtf/mus_musculus/Mus_musculus.GRCm39.103.gtf.gz Fasta:ftp.ensembl.org/pub/release103/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
Or shell I use Mus_musculus.GRCm39.dna.toplevel.fa.gz for fasta to make Generating genome indexes in STAR? STAR --runMode genomeGenerate --runThreadN 8 --genomeDir index_reference --genomeFastaFiles Mus_musculus.GRCm39.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm39.103.gtf
Thank you for your help!