I am trying to create a RSEM index, but am running into an issue with the genome fasta file. When I download Mus_musculus.GRCm38.dna.primary_assembly.fa.gz from ftp.ensembl, it unzips to Mus_musculus.GRCm38.dna.chromosome.1.fa and I get an error that chromosomes are missing. I am using this build because this is the one I used for a previous RNAseq replicate and I want to be consistant. HOWEVER, whem I download the new build (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) and unzip it, it unzips to the coreect contents "Mus_musculus.GRCm39.dna.primary_assembly.fa".
Can anyone tell me what is happening here? And is there another source where I can download the correct Mus_musculus.GRCm38.dna.primary_assembly.fa.gz file? I already mapped all my reads to the star index created using this specific file/build before I realized this issue during RSEM, so I would rather not do it all again.