10x Genomics
Single Cell Gene Expression

Cell Ranger, printed on 11/21/2024

Build Notes for Reference Packages

10x Genomics offers pre-built Cell Ranger reference packages from the downloads page. For purposes of reproducibility, the exact build steps are provided here.

References - 2020-A (July 7, 2020)

Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Human and mouse reference, GRCh38 and mm10 (versions as above)

References - 3.1.0 (July 24, 2019)

Human and mouse reference, GRCh38 (Ensembl 93) and mm10 (Ensembl 93)

References - 3.0.0 (November 19, 2018)

Human reference, GRCh38 (Ensembl 93)
Human reference, hg19 (Ensembl 87)
Mouse reference, mm10 (Ensembl 93)
Human and mouse reference, hg19 (Ensembl 87) and mm10 (Ensembl 93)

References - 2.1.0 (February 7, 2018)

Mouse reference, mm10 (Ensembl 84)
Human and mouse reference, hg19 (Ensembl 82) and mm10 (Ensembl 84)

References - 1.2.0 (November 16, 2016)

Human reference, GRCh38 (Ensembl 84)
Human reference, hg19 (Ensembl 82)
Mouse reference, mm10 (Ensembl 84)
Human and mouse reference, hg19 (Ensembl 82) and mm10 (Ensembl 84)
ERCC reference, ercc92

References - 2020-A (July 8, 2020)

Human reference, GRCh38

# Genome metadata
genome="GRCh38"
version="2020-A"


# Set up source and build directories
build="GRCh38-2020-A_build"
mkdir -p "$build"


# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"


fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.v32.primary_assembly.annotation.gtf"


if [ ! -f "$fasta_in" ]; then
    curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
    curl -sS "$gtf_url" | zcat > "$gtf_in"
fi


# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCh38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "KI270728.1" have the same names in both versions.
#
# Input FASTA:
#   >1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
#
# Output FASTA:
#   >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochrondrial chromosome
cat "$fasta_in" \
    | sed -E 's/^>(\S+).*/>\1 \1/' \
    | sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
    | sed -E 's/^>MT />chrM /' \
    > "$fasta_modified"


# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
#
# Input GTF:
#     ... gene_id "ENSG00000223972.5"; ...
# Output GTF:
#     ... gene_id "ENSG00000223972"; gene_version "5"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
    | sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
    | sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
    | sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
    > "$gtf_modified"


# Define string patterns for GTF tags
# NOTES:
# - Since GENCODE release 31/M22 (Ensembl 97), the "lincRNA" and "antisense"
#   biotypes are part of a more generic "lncRNA" biotype.
# - These filters are relevant only to GTF files from GENCODE. The GTFs from
#   Ensembl release 98 have the following differences:
#   - The names "gene_biotype" and "transcript_biotype" are used instead of
#     "gene_type" and "transcript_type".
#   - Readthrough transcripts are present but are not marked with the
#     "readthrough_transcript" tag.
#   - Only the X chromosome versions of genes in the pseudoautosomal regions
#     are present, so there is no "PAR" tag.
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
PAR_PATTERN="tag \"PAR\""


# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
#   - allowable gene_type (biotype)
#   - allowable transcript_type (biotype)
#   - no "PAR" tag (only present for Y chromosome PAR)
#   - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
    | awk '$3 == "transcript"' \
    | grep -E "$GENE_PATTERN" \
    | grep -E "$TX_PATTERN" \
    | grep -Ev "$READTHROUGH_PATTERN" \
    | grep -Ev "$PAR_PATTERN" \
    | sed -E 's/.*(gene_id "[^"]+").*/\1/' \
    | sort \
    | uniq \
    > "${build}/gene_allowlist"


# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
    >> "$gtf_filtered"


# Create reference package
cellranger mkref --ref-version="$version" \
    --genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered"

Mouse reference, mm10

# Genome metadata
genome="mm10"
version="2020-A"


# Set up source and build directories
build="mm10-2020-A_build"
mkdir -p "$build"


# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"


fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz"
fasta_in="${source}/Mus_musculus.GRCm38.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.vM23.primary_assembly.annotation.gtf"


if [ ! -f "$fasta_in" ]; then
    curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
    curl -sS "$gtf_url" | zcat > "$gtf_in"
fi


# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCm38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "GL456210.1" have the same names in both versions.
#
# Input FASTA:
#   >1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
#
# Output FASTA:
#   >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochrondrial chromosome
cat "$fasta_in" \
    | sed -E 's/^>(\S+).*/>\1 \1/' \
    | sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
    | sed -E 's/^>MT />chrM /' \
    > "$fasta_modified"


# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
#
# Input GTF:
#     ... gene_id "ENSMUSG00000102693.1"; ...
# Output GTF:
#     ... gene_id "ENSMUSG00000102693"; gene_version "1"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
    | sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
    | sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
    | sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
    > "$gtf_modified"


# Define string patterns for GTF tags
# NOTES:
# - Since GENCODE release 31/M22 (Ensembl 97), the "lincRNA" and "antisense"
#   biotypes are part of a more generic "lncRNA" biotype.
# - These filters are relevant only to GTF files from GENCODE. The GTFs from
#   Ensembl release 98 have the following differences:
#   - The names "gene_biotype" and "transcript_biotype" are used instead of
#     "gene_type" and "transcript_type".
#   - Readthrough transcripts are present but are not marked with the
#     "readthrough_transcript" tag.
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""


# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
#   - allowable gene_type (biotype)
#   - allowable transcript_type (biotype)
#   - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
    | awk '$3 == "transcript"' \
    | grep -E "$GENE_PATTERN" \
    | grep -E "$TX_PATTERN" \
    | grep -Ev "$READTHROUGH_PATTERN" \
    | sed -E 's/.*(gene_id "[^"]+").*/\1/' \
    | sort \
    | uniq \
    > "${build}/gene_allowlist"


# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
    >> "$gtf_filtered"


# Create reference package
cellranger mkref --ref-version="$version" \
    --genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered"

Human and mouse reference dataset, GRCh38 and mm10

#################### SETUP ####################


human_genome="GRCh38"
mouse_genome="mm10"
version="2020-A"


build="GRCh38_and_mm10-2020-A_build"
mkdir -p "$build"


# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"


human_fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
human_fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
human_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz"
human_gtf_in="${source}/gencode.v32.primary_assembly.annotation.gtf"
mouse_fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz"
mouse_fasta_in="${source}/Mus_musculus.GRCm38.dna.primary_assembly.fa"
mouse_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz"
mouse_gtf_in="${source}/gencode.vM23.primary_assembly.annotation.gtf"


if [ ! -f "$human_fasta_in" ]; then
    curl -sS "$human_fasta_url" | zcat > "$human_fasta_in"
fi
if [ ! -f "$human_gtf_in" ]; then
    curl -sS "$human_gtf_url" | zcat > "$human_gtf_in"
fi
if [ ! -f "$mouse_fasta_in" ]; then
    curl -sS "$mouse_fasta_url" | zcat > "$mouse_fasta_in"
fi
if [ ! -f "$mouse_gtf_in" ]; then
    curl -sS "$mouse_gtf_url" | zcat > "$mouse_gtf_in"
fi


# String patterns used for both genomes
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"


BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
PAR_PATTERN="tag \"PAR\""


#################### HUMAN ####################
# Please see the GRCh38-2020-A build documentation for details on these steps.


# Process FASTA -- translate chromosome names
human_fasta_modified="$build/$(basename "$human_fasta_in").modified"
cat "$human_fasta_in" \
    | sed -E 's/^>(\S+).*/>\1 \1/' \
    | sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
    | sed -E 's/^>MT />chrM /' \
    > "$human_fasta_modified"


# Process GTF -- split Ensembl IDs from version suffixes
human_gtf_modified="$build/$(basename "$human_gtf_in").modified"
cat "$human_gtf_in" \
    | sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
    | sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
    | sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
    > "$human_gtf_modified"


# Process GTF -- filter based on gene/transcript tags
cat "$human_gtf_modified" \
    | awk '$3 == "transcript"' \
    | grep -E "$GENE_PATTERN" \
    | grep -E "$TX_PATTERN" \
    | grep -Ev "$READTHROUGH_PATTERN" \
    | grep -Ev "$PAR_PATTERN" \
    | sed -E 's/.*(gene_id "[^"]+").*/\1/' \
    | sort \
    | uniq \
    > "${build}/gene_allowlist"


human_gtf_filtered="${build}/$(basename "$human_gtf_in").filtered"
grep -E "^#" "$human_gtf_modified" > "$human_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$human_gtf_modified" \
    >> "$human_gtf_filtered"


#################### MOUSE ####################
# Please see the mm10-2020-A build documentation for details on these steps.


# Process FASTA -- translate chromosome names
mouse_fasta_modified="$build/$(basename "$mouse_fasta_in").modified"
cat "$mouse_fasta_in" \
    | sed -E 's/^>(\S+).*/>\1 \1/' \
    | sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
    | sed -E 's/^>MT />chrM /' \
    > "$mouse_fasta_modified"


# Process GTF -- split Ensembl IDs from version suffixes
mouse_gtf_modified="$build/$(basename "$mouse_gtf_in").modified"
cat "$mouse_gtf_in" \
    | sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
    | sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
    | sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
    > "$mouse_gtf_modified"


# Process GTF -- filter based on gene/transcript tags
cat "$mouse_gtf_modified" \
    | awk '$3 == "transcript"' \
    | grep -E "$GENE_PATTERN" \
    | grep -E "$TX_PATTERN" \
    | grep -Ev "$READTHROUGH_PATTERN" \
    | sed -E 's/.*(gene_id "[^"]+").*/\1/' \
    | sort \
    | uniq \
    > "${build}/gene_allowlist"


mouse_gtf_filtered="${build}/$(basename "$mouse_gtf_in").filtered"
grep -E "^#" "$mouse_gtf_modified" > "$mouse_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$mouse_gtf_modified" \
    >> "$mouse_gtf_filtered"


#################### MKREF ####################


cellranger mkref --ref-version="$version" \
    --genome="$human_genome" --fasta="$human_fasta_modified" --genes="$human_gtf_filtered" \
    --genome="$mouse_genome" --fasta="$mouse_fasta_modified" --genes="$mouse_gtf_filtered"

References - 3.1.0 (July 24, 2019)

Human and mouse reference dataset, GRCh38 and mm10 (includes human and mouse V(D)J genes)

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 19, 2018)

Human reference, GRCh38

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

Human reference, hg19

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

Mouse reference, mm10 (includes mouse V(D)J genes)

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

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

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)

Mouse reference, mm10 (includes mouse V(D)J genes)

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

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

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)

Human reference, GRCh38

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

Human reference, hg19

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

Mouse reference, mm10

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

Human and mouse reference, hg19 and mm10

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

ERCC reference dataset, ercc92

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

Cell Ranger

Loupe

10x Genomics
Single Cell Gene Expression

Build Notes for Reference Packages

References - 2020-A (July 7, 2020)

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 - 2020-A (July 8, 2020)

Human reference, GRCh38

Mouse reference, mm10

Human and mouse reference dataset, GRCh38 and mm10

References - 3.1.0 (July 24, 2019)

Human and mouse reference dataset, GRCh38 and mm10 (includes human and mouse V(D)J genes)

References - 3.0.0 (November 19, 2018)

Human reference, GRCh38

Human reference, hg19

Mouse reference, mm10 (includes mouse V(D)J genes)

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

References - 2.1.0 (February 7, 2018)

Mouse reference, mm10 (includes mouse V(D)J genes)

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

References - 1.2.0 (November 16, 2016)

Human reference, GRCh38

Human reference, hg19

Mouse reference, mm10

Human and mouse reference, hg19 and mm10

ERCC reference dataset, ercc92

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Cell Ranger

Loupe

10x Genomics Single Cell Gene Expression

Build Notes for Reference Packages

References - 2020-A (July 7, 2020)

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 - 2020-A (July 8, 2020)

Human reference, GRCh38

Mouse reference, mm10

Human and mouse reference dataset, GRCh38 and mm10

References - 3.1.0 (July 24, 2019)

Human and mouse reference dataset, GRCh38 and mm10 (includes human and mouse V(D)J genes)

References - 3.0.0 (November 19, 2018)

Human reference, GRCh38

Human reference, hg19

Mouse reference, mm10 (includes mouse V(D)J genes)

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

References - 2.1.0 (February 7, 2018)

Mouse reference, mm10 (includes mouse V(D)J genes)

Human and mouse reference dataset, hg19 and mm10 (includes human and mouse V(D)J genes)

References - 1.2.0 (November 16, 2016)

Human reference, GRCh38

Human reference, hg19

Mouse reference, mm10

Human and mouse reference, hg19 and mm10

ERCC reference dataset, ercc92

10x Genomics
Single Cell Gene Expression