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10x Genomics
Single Cell Gene Expression

Build Notes for Reference Packages

Steps to create the pre-built Cell Ranger reference packages from the downloads page.

References - 3.1.0 (July 24, 2019)

References - 3.0.0 (November 19, 2018)

References - 2.1.0 (February 7, 2018)

References - 1.2.0 (November 16, 2016)


References - 3.1.0 (July 24, 2018)

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
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz gunzip Mus_musculus.GRCm38.93.gtf.gz
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
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.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
cellranger mkref --genome=GRCh38 \ --fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh38.93.filtered.gtf \ --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.93.filtered.gtf \ --ref-version=3.1.0

References - 3.0.0 (November 18, 2018)

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

wget ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz gunzip Homo_sapiens.GRCh37.87.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.87.gtf Homo_sapiens.GRCh37.87.filtered.gtf \ --attribute=gene_biotype:protein_coding \ --attribute=gene_biotype:lincRNA \ --attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \ --fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh37.87.filtered.gtf \ --ref-version=3.0.0

wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz gunzip Mus_musculus.GRCm38.93.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.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
cellranger mkref --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.93.filtered.gtf \ --ref-version=3.0.0

wget ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz gunzip Homo_sapiens.GRCh37.87.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz gunzip Mus_musculus.GRCm38.93.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.87.gtf Homo_sapiens.GRCh37.87.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
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.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
cellranger mkref --genome=hg19 \ --fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh37.87.filtered.gtf \ --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.93.filtered.gtf \ --ref-version=3.0.0

References - 2.1.0 (February 7, 2018)

wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.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
cellranger mkref --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.84.filtered.gtf \ --ref-version=2.1.0

wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz gunzip Homo_sapiens.GRCh37.82.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.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
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.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
cellranger mkref --genome=hg19 \ --fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh37.82.filtered.gtf \ --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.84.filtered.gtf \ --ref-version=2.1.0

References - 1.2.0 (November 16, 2016)

wget ftp://ftp.ensembl.org/pub/release-84/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-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz gunzip Homo_sapiens.GRCh38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh38.84.gtf Homo_sapiens.GRCh38.84.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
cellranger mkref --genome=GRCh38 \ --fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh38.84.filtered.gtf \ --ref-version=1.2.0

wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz gunzip Homo_sapiens.GRCh37.82.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \ --attribute=gene_biotype:protein_coding \ --attribute=gene_biotype:lincRNA \ --attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \ --fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh37.82.filtered.gtf \ --ref-version=1.2.0

wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \ --attribute=gene_biotype:protein_coding \ --attribute=gene_biotype:lincRNA \ --attribute=gene_biotype:antisense
cellranger mkref --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.84.filtered.gtf \ --ref-version=1.2.0

wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz gunzip Homo_sapiens.GRCh37.82.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \ --attribute=gene_biotype:protein_coding \ --attribute=gene_biotype:lincRNA \ --attribute=gene_biotype:antisense
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \ --attribute=gene_biotype:protein_coding \ --attribute=gene_biotype:lincRNA \ --attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \ --fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --genes=Homo_sapiens.GRCh37.82.filtered.gtf \ --genome=mm10 \ --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \ --genes=Mus_musculus.GRCm38.84.filtered.gtf \ --ref-version=1.2.0

cellranger mkref --genome=ercc92 \
                 --fasta=ercc92.fa \
                 --genes=ercc92.gtf \
                 --ref-version=1.2.0