Example Cell Ranger load scripts

[mjsteinbaugh]

@sjhosui here are the requested Cell Ranger scripts we have used on O2. I've included the sbatch settings for slurm as well.

slurm config

#SBATCH --job-name=cellranger          # Job name
#SBATCH --partition=medium             # Partition name
#SBATCH --time=3-00:00                 # Runtime in D-HH:MM format
#SBATCH --nodes=1                      # Number of nodes (keep at 1)
#SBATCH --ntasks=1                     # Number of tasks per node (keep at 1)
#SBATCH --cpus-per-task=16             # CPU cores requested per task (change for threaded jobs)
#SBATCH --mem=128G                     # Memory needed per node (total)
#SBATCH --error=jobid_%j.err           # File to which STDERR will be written, including job ID
#SBATCH --output=jobid_%j.out          # File to which STDOUT will be written, including job ID
#SBATCH --mail-type=ALL                # Type of email notification (BEGIN, END, FAIL, ALL)

module load bcl2fastq/2.20.0.422
module load cellranger/2.1.1

localcores=$SLURM_CPUS_PER_TASK
localmem=128

mkfastq

# Point to the Illumina BCL run directory
# Use a CSV file to specify the samples (see 10X website for examples)
# cellranger mkfastq --help
illumina_bcl_dir="AFCHK2VYCCXY"
csv="mkfastq.csv"
cellranger mkfastq \
    --run="${illumina_bcl_dir}" \
    --csv="${csv}" \
    --localcores="${localcores}" \
    --localmem="${localmem}"

count

Note that --nosecondary here will skip the automatic downstream clustering.

fastqs="MKFASTQ_DIR"
transcriptome="/n/data1/cores/bcbio/10x_genomics/cellranger/refdata/XXX"

# Repeat this command per sample
cellranger count \
    --id=WT-A-CML6022-p8 \
    --sample=WT-A-CML6022-p8 \
    --fastqs="${fastqs}"  \
    --transcriptome="${transcriptome}" \
    --localcores="${localcores}" \
    --localmem="${localmem}" \
    --nosecondary

aggr

Aggregating Multiple Libraries

Run this after the per sample data processing has completed.

cellranger aggr \
  --id="aggr" \
  --csv="aggr.csv" \
  --normalize="mapped" \
  --localcores="${SLURM_CPUS_PER_TASK}" \
  --localmem=128 \
  --nosecondary