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linux code.txt
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export PATH=/home/soft/cellranger-2.1.1:$PATH
cellranger count --id=m07 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m07
cellranger count --id=m08 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m08
cellranger count --id=m09 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m09
cellranger count --id=m10 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m10
cellranger count --id=m10h --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m10h
cellranger count --id=m11h --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m11h
cellranger count --id=m12h --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m12h
cellranger count --id=m12 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m12
cellranger count --id=m13 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m13
cellranger count --id=m14 --transcriptome=/home/soft/GRCm38.89 --fastqs=fastq/m14
cellranger aggr --id=MPL-10 --csv=mpl-10.csv --normalize=mapped
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m7 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m8 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m9 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m10 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m10h /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m11h /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m12h /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m12 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m13 /home/soft/GRCm38.89/genes/genes.gtf
velocyto run10x -m /home/soft/mm10_rmsk.gtf GRCm38_89-m14 /home/soft/GRCm38.89/genes/genes.gtf
export PATH=/home/soft/cellranger-7.0.0:$PATH
cellranger count --id=V3-E7 --transcriptome=/home/soft/GRCm38.89 --fastqs=V3-E7
cellranger count --id=V3-E8 --transcriptome=/home/soft/GRCm38.89 --fastqs=V3-E8
cellranger count --id=V3-E9 --transcriptome=/home/soft/GRCm38.89 --fastqs=V3-E9 --force-cells=10000
cellranger count --id=V3-E13 --transcriptome=/home/soft/GRCm38.89 --fastqs=V3-E13
cellranger count --id=V3-E11 --transcriptome=/home/soft/GRCm38.89 --fastqs=V3-E11
cellranger aggr --id=MTR-V3-5 --csv=MTR-V3-5.csv --normalize=mapped