run_cell_ranger

run.sh

# convert Docker container to Singularity format
singularity build cell_ranger_3.1.0.sif docker://romanhaa/cell_ranger:3.1.0

# create index for Cell Ranger
# - modify "/hpcnfs" to your file system
singularity exec --bind /hpcnfs cell_ranger_3.1.0.simg \
cellranger mkref \
--genome=cell_ranger_3.1.0 \
--fasta=GRCh38.primary_assembly.genome.fa \
--genes=gencode.v32.annotation.gtf \
--nthreads=10 \
--memgb=8

# generate transcript count table from FASTQ files
# - modify "/hpcnfs" to your file system
singularity exec --bind /hpcnfs cell_ranger_3.1.0.simg \
cellranger count \
--id=pbmc_10k_v3 \
--transcriptome=<path_to_reference_genome> \
--fastqs=<path_to_FASTQ_files> \
--sample=pbmc_10k_v3 \
--expect-cells=10000 \
--jobmode=local \
--localcores=20 \
--localmem=100 \
--mempercore=5