Cell Ranger and Cell Ranger ATAC - RegnerM2015/scBreast_scRNA_scATAC_2024 GitHub Wiki

Cell Ranger (version 3.1.0)

Demultiplex Illumina base calls into FASTQ files with cellranger mkfastq:

/scripts/example_cellranger_mkfastq-patients_5_and_7.sh

#!/usr/bin/env bash

#SBATCH --job-name H2YT7BGXB
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output H2YT7BGXB_demultiplex.job.out
#SBATCH --error H2YT7BGXB_demultiplex.job.err

DATA=/datastore/nextgenout5/share/labs/bioinformatics/seqware/francolab_10x_copy
OUT=/datastore/nextgenout5/share/labs/francolab/scRNA-seq_Breast.05.28.2019

cellranger mkfastq --id=H2YT7BGXB \
                   --run=${DATA}/190524_NS500270_0300_AH2YT7BGXB \
                   --csv=${OUT}/Samplesheet.csv \
                   --qc \
                   --localcores=16

Run cellranger count for Patient 5 with refdata-cellranger-GRCh38-3.0.0:

/scripts/example_cellranger_count-patient_5.sh

#!/usr/bin/env bash

#SBATCH --job-name HT-35A4AL-RNA_MAY2019_G5
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output HT-35A4AL-RNA_MAY2019_G5.cellranger-count.job.update.out 
#SBATCH --error HT-35A4AL-RNA_MAY2019_G5.cellranger-count.job.update.err 

DATA=/datastore/nextgenout5/share/labs/francolab/Data

cellranger count  --id=HT-35A4AL-RNA_MAY2019_G5_Update \
                      --fastqs=./fastq_path/H2YT7BGXB/HT-35A4AL-RNA_MAY2019_G5 \
                      --transcriptome=${DATA}/refdata-cellranger-GRCh38-3.0.0 \
                      --sample=HT-35A4AL-RNA_MAY2019_G5 \
                      --localcores=16 \
                      --localmem=80

Run cellranger count for Patient 7 with refdata-cellranger-GRCh38-3.0.0:

/scripts/example_cellranger_count-patient_7.sh

#!/usr/bin/env bash

#SBATCH --job-name HT-35EE8L-RNA_MAY2019_G6
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output HT-35EE8L-RNA_MAY2019_G6.cellranger-count.job.update.out 
#SBATCH --error HT-35EE8L-RNA_MAY2019_G6.cellranger-count.job.update.err 

DATA=/datastore/nextgenout5/share/labs/francolab/Data

cellranger count  --id=HT-35EE8L-RNA_MAY2019_G6_Update \
                      --fastqs=./fastq_path/H2YT7BGXB/HT-35EE8L-RNA_MAY2019_G6 \
                      --transcriptome=${DATA}/refdata-cellranger-GRCh38-3.0.0 \
                      --sample=HT-35EE8L-RNA_MAY2019_G6 \
                      --localcores=16 \
                      --localmem=80

Cell Ranger ATAC (version 1.2.0)

Demultiplex Illumina base calls into FASTQ files with cellranger-atac mkfastq:

/scripts/example_cellranger_atac_mkfastq-patients_5_and_7.sh

#!/usr/bin/env bash

#SBATCH --job-name H2NFLBGXB
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output H2NFLBGXB_demultiplex.job.out
#SBATCH --error H2NFLBGXB_demultiplex.job.err

DATA=/datastore/nextgenout5/share/labs/bioinformatics/seqware/francolab_10x_copy
OUT=/datastore/nextgenout5/share/labs/francolab/scATAC-seq_Breast.05.29.2019

cellranger-atac mkfastq --id=H2NFLBGXB \
                        --run=${DATA}/190528_NS500270_0301_AH2NFLBGXB \
                        --csv=${OUT}/Samplesheet.csv \
                        --qc \
                        --localcores=16

Run cellranger-atac count for Patient 5 with refdata-cellranger-atac-GRCh38-1.2.0:

/scripts/example_cellranger_atac_count-patient_5.sh

#!/usr/bin/env bash

#SBATCH --job-name HT-35A4AL-ATAC_MAY2019_A5
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output HT-35A4AL-ATAC_MAY2019_A5.cellranger-count.job.update.out 
#SBATCH --error HT-35A4AL-ATAC_MAY2019_A5.cellranger-count.job.update.err 

DATA=/datastore/nextgenout5/share/labs/francolab/Data

cellranger-atac count --id=HT-35A4AL-ATAC_MAY2019_A5_Update \
                      --fastqs=./fastq_path/H2NFLBGXB/HT-35A4AL-ATAC_MAY2019_A5 \
                      --reference=${DATA}/refdata-cellranger-atac-GRCh38-1.2.0 \
                      --sample=HT-35A4AL-ATAC_MAY2019_A5 \
                      --localcores=16

Run cellranger-atac count for Patient 7 with refdata-cellranger-atac-GRCh38-1.2.0:

/scripts/example_cellranger_atac_count-patient_7.sh

#!/usr/bin/env bash

#SBATCH --job-name HT-35EE8L-ATAC_MAY2019_A6
#SBATCH -c 16
#SBATCH --mem 80g
#SBATCH --partition allnodes
#SBATCH --output HT-35EE8L-ATAC_MAY2019_A6.cellranger-count.job.update.out 
#SBATCH --error HT-35EE8L-ATAC_MAY2019_A6.cellranger-count.job.update.err 

DATA=/datastore/nextgenout5/share/labs/francolab/Data

cellranger-atac count --id=HT-35EE8L-ATAC_MAY2019_A6_Update \
                      --fastqs=./fastq_path/H2NFLBGXB/HT-35EE8L-ATAC_MAY2019_A6 \
                      --reference=${DATA}/refdata-cellranger-atac-GRCh38-1.2.0 \
                      --sample=HT-35EE8L-ATAC_MAY2019_A6 \
                      --localcores=16