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!
The genome construction step line looks good. Also consider including the `--sjdbOverhang` parameter. While the default value of 99 is usually fine, as stated in STAR's manual this should be chosen according to your maximum read length in the dataset by subtracting 1. So, if you have 100 nt reads, `--sjdbOverhang 99` is fine.

 If you performed trimming and has variable read lengths, then you choose this value according to `max(readLength-1)`. So if you have reads varying from 50-120, you'd have `--sjdbOverhang 119` as optimal parameter.