Cellranger count snippets (version 2)

cellranger_count_scenarios.sh

# Some universal variables
NCELLS=6000
OUTPUT_NAME="nice-name"
FASTQ_DIR="/path/to/fastqs"
REFERENCE_GENOME="/path/to/reference_dir"
[[ -z "${PBS_NUM_PPN}" ]] && NCORES=20 || NCORES=${PBS_NUM_PPN}

# When reads look like:
# sample-name_S?_L00?_R1_001.fastq.gz
# sample-name_S?_L00?_R2_001.fastq.gz
# sample-name_S?_L00?_I1_001.fastq.gz

SAMPLE_NAME="sample-name"

cellranger count \
    --sample="${SAMPLE_NAME}" \
    --id="${OUTPUT_NAME}" \
    --transcriptome="${REFERENCE_GENOME}" \
    --fastqs="${FASTQ_DIR}" \
    --localcores="${NCORES}" \
    --expect-cells="${NCELLS}" \
    --disable-ui || exit 1


# When reads look like:
# sample-name-1_S?_L00?_R1_001.fastq.gz
# sample-name-1_S?_L00?_R2_001.fastq.gz
# sample-name-1_S?_L00?_I1_001.fastq.gz
# ...
# sample-name-n_S?_L00?_R1_001.fastq.gz
# sample-name-n_S?_L00?_R2_001.fastq.gz
# sample-name-n_S?_L00?_I1_001.fastq.gz

SAMPLE_LIST="sample-name-1,sample-name-2,...,sample-name-n"
SAMPLE_NAME="sample-combined"

set -x; cellranger count \
    --id="${SAMPLE_NAME}" \
    --transcriptome="${REFERENCE_GENOME}" \
    --fastqs="${FASTQ_DIR}" \
    --expect-cells="${NCELLS}" \
    --localcores="${NCORES}" \
    --sample="${SAMPLE_LIST}" \
    --disable-ui || exit 1


# When reads look like:
# sample-name_index1_S?_L00?_R1_001.fastq.gz
# sample-name_index1_S?_L00?_R2_001.fastq.gz
# sample-name_index1_S?_L00?_I1_001.fastq.gz
...
# sample-name_indexn_S?_L00?_R1_001.fastq.gz
# sample-name_indexn_S?_L00?_R2_001.fastq.gz
# sample-name_indexn_S?_L00?_I1_001.fastq.gz

INDEX_LIST="index1,...,indexn"
SAMPLE_NAME="sample-name"

cellranger count \
    --id="${SAMPLE_NAME}" \
    --transcriptome="${INDEX}" \
    --fastqs="${FASTQ_PATH}" \
    --expect-cells="${NCELLS}" \
    --localcores="${NCORES}" \
    --indices=${INDEX_LIST} \
    --disable-ui || exit 1


# When reads look like:
# sample-name_index1_S?_L00?_R1_001.fastq.gz
# sample-name_index1_S?_L00?_R2_001.fastq.gz
# sample-name_index1_S?_L00?_I1_001.fastq.gz
...
# sample-name_indexn_S?_L00?_R1_001.fastq.gz
# sample-name_indexn_S?_L00?_R2_001.fastq.gz
# sample-name_indexn_S?_L00?_I1_001.fastq.gz
# read-I1_si-AGGGCGGT_lane-001-chunk-001.fastq.gz
# read-I1_si-AGGGCGGT_lane-002-chunk-000.fastq.gz  
# read-I1_si-AGGGCGGT_lane-003-chunk-003.fastq.gz  
# read-I1_si-AGGGCGGT_lane-004-chunk-002.fastq.gz
...
# read-I2_si-AGGGCGGT_lane-001-chunk-001.fastq.gz
# read-I2_si-AGGGCGGT_lane-002-chunk-000.fastq.gz  
# read-I2_si-AGGGCGGT_lane-003-chunk-003.fastq.gz  
# read-I2_si-AGGGCGGT_lane-004-chunk-002.fastq.gz  
...
# read-RA_si-AGGGCGGT_lane-001-chunk-001.fastq.gz
# read-RA_si-AGGGCGGT_lane-002-chunk-000.fastq.gz  
# read-RA_si-AGGGCGGT_lane-003-chunk-003.fastq.gz  
# read-RA_si-AGGGCGGT_lane-004-chunk-002.fastq.gz  

INDEX_LIST="AGGGCGGT,..."
LANE_LIST="1,2,..."
SAMPLE_NAME="sample-name"

cellranger count \
    --id="${SAMPLE_NAME}" \
    --transcriptome="${INDEX}" \
    --fastqs="${FASTQ_PATH}" \
    --expect-cells="${NCELLS}" \
    --localcores="${NCORES}" \
    --indices=${INDEX_LIST} \
    --lanes=${LANE_LIST} \
    --disable-ui || exit 1