make_cellranger_index.sh

#!/bin/bash
#SBATCH --partition=general
#SBATCH --job-name=cr_index
#SBATCH --nodes=1
#SBATCH --mem=64000
#SBATCH --cpus=8
#SBATCH --time=12:00:00
#SBATCH --mail-type=ALL

module load cellranger

#wget ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
#gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz


#wget ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz
#gunzip Homo_sapiens.GRCh38.93.gtf.gz

echo started mkgtf

cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf \
                 --attribute=gene_biotype:protein_coding \
                 --attribute=gene_biotype:lincRNA \
                 --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

echo started mkref

cellranger mkref --genome=GRCh38 \
                 --fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \
                 --genes=Homo_sapiens.GRCh38.93.filtered.gtf \
                 --ref-version=3.0.0