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Cellranger reference genome

Updated: June 4th, 2020 (update mm & hs)

Huitian (Yolanda) Diao
cellranger-3.1.0
Location: /gpfs/group/pipkin/hdiao/ref_resources
How to choose reference genome

1. Mus Musclus

1.1 Input files

Download from Ensembl

  • DNA fasta file: release 100, last update 3/5/20
  • GTF file: release 100, last update 3/9/20

1.2 Build reference genome

#!/bin/bash
# Filter gtf 
# https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#mkgtf

module load cellranger

wkdir=/gpfs/group/pipkin/hdiao/ref_resources/mm/release100
cd $wkdir

cellranger mkgtf Mus_musculus.GRCm38.100.gtf Mus_musculus.GRCm38.100.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=GRCm38 \
                 --fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
                 --genes=Mus_musculus.GRCm38.100.filtered.gtf \
                 --ref-version=3.1.0

2. Homo Sapien

2.1 Input files

Download from Ensembl

  • DNA fasta file (use primary assembly as cellranger suggested): last update 3/4/20
  • GTF file: last update 3/7/20

2.2 Build reference genome

#!/bin/bash
# Filter gtf 
# https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#mkgtf

module load cellranger

wkdir=/gpfs/group/pipkin/hdiao/ref_resources/hs/release100
cd $wkdir

cellranger mkgtf Homo_sapiens.GRCh38.100.gtf Homo_sapiens.GRCh38.100.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.GRCh38.100.filtered.gtf \
                 --ref-version=3.1.0