GSE279254 Processing Pipeline

Publication

Nature (2025) — PMID 39843748

Dataset

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted [snRNA-Seq]

1. 1

   cellranger was used to process the raw sequencing files to generate count matrices per cell

   Cell Ranger vNot specified

   $ Bash example

   # Install Cell Ranger (example for version 7.1.0)
   # wget https://cf.10xgenomics.com/releases/cell-ranger/cellranger-7.1.0.tar.gz
   # tar -xzf cellranger-7.1.0.tar.gz
   # export PATH=/path/to/cellranger-7.1.0:$PATH
   
   # Example: Download a human transcriptome reference (e.g., GRCh38-2020-A)
   # mkdir -p /path/to/references
   # wget -O /path/to/references/refdata-gex-GRCh38-2020-A.tar.gz https://cf.10xgenomics.com/releases/cell-ranger/refdata-gex-GRCh38-2020-A.tar.gz
   # tar -xzf /path/to/references/refdata-gex-GRCh38-2020-A.tar.gz -C /path/to/references
   
   # Define variables
   SAMPLE_ID="my_sample"
   FASTQ_DIR="/path/to/raw_fastqs"
   TRANSCRIPTOME_REF="/path/to/references/refdata-gex-GRCh38-2020-A"
   
   # Run cellranger count to generate count matrices
   cellranger count \
     --id=${SAMPLE_ID} \
     --transcriptome=${TRANSCRIPTOME_REF} \
     --fastqs=${FASTQ_DIR} \
     --sample=${SAMPLE_ID}
   

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