单细胞转录组分析--修改cellranger适合大size基因组

1. 建立genome的索引

Note: /gpfs02/home/jingjing/software/cellranger-4.0.0/lib/python/cellranger/reference.py  修改参数来适应大基因组

/gpfs02/home/jingjing/software/cellranger-4.0.0/bin/cellranger mkref --genome refdata --nthreads 30 --fasta N.tab.all.fa --genes N.tab.all.gtf

2. 运行cellranger count

/gpfs02/home/jingjing/software/cellranger-4.0.0/bin/cellranger count --id run_count_1kpbmcs --fastqs pbmc_1k_v3_fastqs/ --sample pbmc_1k_v3 --transcriptome refdata-cellranger-GRCh38-3.0.0/