cellranger_mkgtf.sh

#!/bin/bash
#SBATCH --job-name=mkgtf
#SBATCH -o /home/zhuyong/cellranger/code/logs/%j_%x.log
#SBATCH -e /home/zhuyong/cellranger/code/logs/%j_%x.log
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4 # specify number of CPUs to use here
#SBATCH --mem-per-cpu=10gb

module load cellranger/7.1.0
cellranger mkgtf /home/zhuyong/cellranger/00ref/genomic.gtf  /home/zhuyong/cellranger/00ref/genomic_filtered.gtf   \
                   --attribute=gene_biotype:protein_coding \
                   --attribute=gene_biotype:lncRNA \
                   --attribute=gene_biotype:antisense \
                   --attribute=gene_biotype:IG_LV_gene \
                   --attribute=gene_biotype:IG_V_gene \
                   --attribute=gene_biotype:IG_V_pseudogene \
                   --attribute=gene_biotype:IG_D_gene \
                   --attribute=gene_biotype:IG_J_gene \
                   --attribute=gene_biotype:IG_J_pseudogene \
                   --attribute=gene_biotype:IG_C_gene \
                   --attribute=gene_biotype:IG_C_pseudogene \
                   --attribute=gene_biotype:TR_V_gene \
                   --attribute=gene_biotype:TR_V_pseudogene \
                   --attribute=gene_biotype:TR_D_gene \
                   --attribute=gene_biotype:TR_J_gene \
                   --attribute=gene_biotype:TR_J_pseudogene \
                   --attribute=gene_biotype:TR_C_gene