CellRanger on KHW NAR scRNAseq data from 20240724
Sample information
| Sample # | Customer Sample Name | BaseSpace Sample ID | Flow Cell Type | Read Type | Total number of clusters (reads) per sample |
|---|---|---|---|---|---|
| 1 | gfas_control | AndradeRodriguez-19876-001_GEX3 | 10B-300 | paired-end,151 | 581,421,834 |
| 2 | gfas_bleach | AndradeRodriguez-19876-002_GEX3 | 10B-300 | paired-end,151 | 636,439,053 |
Upload files
scp -r /Users/cnidarianimmunity/Desktop/KHW/Andrade_Rodriguez-01-07-19876-425120288/2024* kxw755@pegasus.ccs.miami.edu:/nethome/kxw755
Count 001
nano count_001.job
#BSUB -J count_19876-001
#BSUB -q bigmem
#BSUB -P dark_genes
#BSUB -n 16
#BSUB -W 120:00
#BSUB -R "rusage[mem=15000]"
#BSUB -u kxw755@earth.miami.edu
#BSUB -o count_19876-001.out
#BSUB -e count_19876-001.err
#BSUB -B
#BSUB -N
###################################################################
module load cellranger/8.0.0
cellranger count \
--id=19876-001 \
--transcriptome=/nethome/kxw755/Gfas_v1/gfas \
--fastqs=/nethome/kxw755/20240724_AndradeRodriguez-19876-001 \
--sample=AndradeRodriguez-19876-001_GEX3 \
--create-bam=true
bsub < count_001.job
Export
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-001/19876-001/outs/web_summary.html /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-001_web_summary.html
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-001/19876-001/outs/filtered_feature_bc_matrix.h5 /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-001_filtered_feature_bc_matrix.h5
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-001/19876-001/outs/metrics_summary.csv /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-001_metrics_summary.csv
Count 002
nano count_002.job
#BSUB -J count_19876-002
#BSUB -q bigmem
#BSUB -P dark_genes
#BSUB -n 16
#BSUB -W 120:00
#BSUB -R "rusage[mem=15000]"
#BSUB -u kxw755@earth.miami.edu
#BSUB -o count_19876-002.out
#BSUB -e count_19876-002.err
#BSUB -B
#BSUB -N
###################################################################
module load cellranger/8.0.0
cellranger count \
--id=19876-002 \
--transcriptome=/nethome/kxw755/Gfas_v1/gfas \
--fastqs=/nethome/kxw755/20240724_AndradeRodriguez-19876-002 \
--sample=AndradeRodriguez-19876-002_GEX3 \
--create-bam=true
bsub < count_002.job
Export
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-002/19876-002/outs/web_summary.html /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-002_web_summary.html
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-002/19876-002/outs/filtered_feature_bc_matrix.h5 /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-002_filtered_feature_bc_matrix.h5
scp -r kxw755@pegasus.ccs.miami.edu:/nethome/kxw755/20240724_AndradeRodriguez-19876-002/19876-002/outs/metrics_summary.csv /Users/kxw755/Desktop/DarkGenes/20240724_CellRanger/20240724_AndradeRodriguez-19876-002_metrics_summary.csv
Summary Table
Written on July 24, 2024