Murine B-cells Bioinformatics

#Got mouse genome and immune cell annotation
wget ftp://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-110/gtf/mus_musculus/Mus_musculus.GRCm39.110.gtf.gz
#unzipped
gunzip Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm39.110.gtf.gz
#loaded modules
module load arcc/1.0 zlib-ng/2.1.4_zen4 miniconda3/24.3.0
#activated single cell rna conda environment
conda activate scrna-env
#Created reference genome
STAR --runThreadN 8 \
     --runMode genomeGenerate \
     --genomeDir ./ \
     --genomeFastaFiles Mus_musculus.GRCm39.dna.primary_assembly.fa \
     --sjdbGTFfile Mus_musculus.GRCm39.110.gtf \
     --sjdbOverhang 99
#rezipped
gzip Mus_musculus.GRCm39.dna.primary_assembly.fa
gzip Mus_musculus.GRCm39.110.gtf
#exit conda
conda deactivate
#move to rawdata directory
cd /project/gtl/data/distribution/Pascual/1Pasc/rawdata
#process samples
sbatch Illumina3rna.sh