run_cellranger.pbs

# Run cellranger v7.1.0
cellranger count --id=sample001 \
    --transcriptome=/scratch/antwerpen/208/vsc20830/ref_genome/refdata-gex-GRCh38-2020-A \
    --fastqs=/scratch/antwerpen/208/vsc20830/fastq/SRR28562212 \
    --sample=CHB20 \
    --localcores=28 \
    --localmem=112

#NOTES for cellranger options
#'--id' sets output dir
#'--sample' contains the filename in this format: 'CHB20' for 'CHB20_S1_L001_R1_001.fastq.gz

# Sample identifier key 
##################################
#"sample001","SRR28562212","CHB20"
#"sample002","SRR28562213","CHB14"
#"sample003","SRR28562214","CHB13"
#"sample004","SRR28562215","CHB9" 
#"sample005","SRR28562216","CHB8" 
#"sample006","SRR28562227","CHB7" 
#"sample007","SRR28562238","CHB5" 
#"sample008","SRR28562246","FC9"  
#"sample009","SRR28562248","FC6"  
#"sample010","SRR28562249","CHB4" 
#"sample011","SRR28562250","FC5"  
#"sample012","SRR28562251","FC4"  
#"sample013","SRR28562252","FC3"  
#"sample014","SRR28562253","FC2"  
#"sample015","SRR28562254","FC1"  
#"sample016","SRR28562255","CHB31"
#"sample017","SRR28562256","CHB30"
#"sample018","SRR28562257","CHB28"
#"sample019","SRR28562258","CHB24"
#"sample020","SRR28562259","CHB23"
#"sample021","SRR28562260","CHB3" 
#"sample022","SRR28562261","CHB2" 
#"MISSING_SRA","SRR28562247","FC8"