Databases provide several variations of the FASTA genome. Choosing the wrong type can severely slow down your alignment tools or cause software crashes.
# Navigate to your project reference directory mkdir -p mouse_reference && cd mouse_reference # Download the GRCm39 primary assembly nucleotide FASTA wget ftp://ftp.ensembl.org/pub/release-111/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz # Decompress the file for use gunzip Mus_musculus.GRCm39.dna.primary_assembly.fa.gz Use code with caution. Method B: Downloading from UCSC (mm39) mouse genome fasta download
If your pipeline requires the chr naming prefix, download the complete block directly from UCSC. Databases provide several variations of the FASTA genome
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