Cell Ranger ATAC, printed on 12/26/2024
Steps to create the pre-built Cell Ranger ATAC reference packages from the downloads page.
# Genome metadata
genome="GRCh38"
version="2020-A"
# Set up source and build directories
build="${genome}-${version}-build"
mkdir -p "$build"
# Download source files if they do not exist in reference-sources/ folder
source="${genome}-${version}-reference-sources"
mkdir -p "$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"
motifs_url="https://jaspar.genereg.net/download/data/2018/CORE/JASPAR2018_CORE_non-redundant_pfms_jaspar.txt"
motifs_in="${source}/JASPAR2018_CORE_non-redundant_pfms_jaspar.txt"
if [ ! -f "$fasta_in" ]; then
curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
curl -sS "$gtf_url" | zcat > "$gtf_in"
fi
if [ ! -f "$motifs_in" ]; then
curl -sS "$motifs_url" > "$motifs_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";/' \
> "$gtf_modified"
# Define string patterns for GTF tags
# NOTES:
# - Since GENCODE release 31/M22 (Ensembl 97), the "lncRNA" and "antisense"
# biotypes are part of a more generic "lncRNA" biotype.
# - These filters are relevant only to GTF files from GENCODE. The GTFs from
# Ensembl release 98 have the following differences:
# - The names "gene_biotype" and "transcript_biotype" are used instead of
# "gene_type" and "transcript_type".
# - Readthrough transcripts are present but are not marked with the
# "readthrough_transcript" tag.
# - Only the X chromosome versions of genes in the pseudoautosomal regions
# are present, so there is no "PAR" tag.
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${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"
# Change motif headers so the human-readable motif name precedes the motif
# identifier. So ">MA0004.1 Arnt" -> ">Arnt_MA0004.1".
motifs_modified="$build/$(basename "$motifs_in").modified"
awk '{
if ( substr($1, 1, 1) == ">" ) {
print ">" $2 "_" substr($1,2)
} else {
print
}
}' "$motifs_in" > "$motifs_modified"
# Create a config file
config_in="${build}/config"
echo """{
organism: \"Homo_sapiens\"
genome: [\""$genome"\"]
input_fasta: [\""$fasta_modified"\"]
input_gtf: [\""$gtf_filtered"\"]
input_motifs: \""$motifs_modified"\"
non_nuclear_contigs: [\"chrM\"]
}""" > "$config_in"
# Create reference package
cellranger-arc mkref --ref-version="$version" \
--config="$config_in"
# Genome metadata
genome="mm10"
version="2020-A"
# Set up source and build directories
build="${genome}-${version}-build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="${genome}-${version}-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="${source}/gencode.vM23.primary_assembly.annotation.gtf"
motifs_url="http://jaspar2018.genereg.net/download/CORE/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt"
motifs_in="${source}/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt"
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
if [ ! -f "$motifs_in" ]; then
curl -sS "$motifs_url" > "$motifs_in"
fi
# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCm38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "GL456210.1" have the same names in both versions.
#
# Input FASTA:
# >1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
#
# Output FASTA:
# >chr1 1
fasta_modified="$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 "lncRNA" 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" \
>> "$gtf_filtered"
# Change motif headers so the human-readable motif name precedes the motif
# identifier. So ">MA0004.1 Arnt" -> ">Arnt_MA0004.1".
motifs_modified="$build/$(basename "$motifs_in").modified"
awk '{
if ( substr($1, 1, 1) == ">" ) {
print ">" $2 "_" substr($1,2)
} else {
print
}
}' "$motifs_in" > "$motifs_modified"
# Create a config file
config_in="${build}/config"
echo """{
organism: \"Mus_musculus\"
genome: [\""$genome"\"]
input_fasta: [\""$fasta_modified"\"]
input_gtf: [\""$gtf_filtered"\"]
input_motifs: \""$motifs_modified"\"
non_nuclear_contigs: [\"chrM\"]
}""" > "$config_in"
# Create reference package
cellranger-arc mkref --ref-version="$version" \
--config="$config_in"