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@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.
@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
mkfastq
count
Note that
--nosecondary
here will skip the automatic downstream clustering.aggr
Aggregating Multiple Libraries
Run this after the per sample data processing has completed.
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