GSE154778 Processing Pipeline

Publication

Nature communications (2023) — PMID 37673892

Dataset

Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues

1. 1

   Cell Ranger

   Cell Ranger vNot specified

   $ Bash example

   # Install Cell Ranger (example, adjust for specific environment and version)
   # Download Cell Ranger from the 10x Genomics website:
   # https://www.10xgenomics.com/support/software/cell-ranger/downloads
   # For example, to install version 8.0.0:
   # wget https://cf.10xgenomics.com/releases/cell-ranger/cellranger-8.0.0.tar.gz
   # tar -xzf cellranger-8.0.0.tar.gz
   # export PATH=/path/to/cellranger-8.0.0:$PATH
   
   # Reference Dataset: Cell Ranger requires a pre-built transcriptome reference.
   # This reference is typically generated once using the 'cellranger mkref' command
   # from a genome FASTA file and a gene annotation GTF file (e.g., from GENCODE or Ensembl).
   # As a placeholder, we'll assume a GRCh38 human transcriptome reference.
   # Example command to build a reference (replace paths and versions as needed):
   # cellranger mkref \
   #     --genome=GRCh38_v8.0.0 \
   #     --fasta=/path/to/GRCh38.primary_assembly.fa \
   #     --genes=/path/to/gencode.v38.annotation.gtf \
   #     --ref-version=8.0.0
   
   # Example: Run cellranger count for a single-cell RNA-seq experiment.
   # Replace 'sample_id', '/path/to/fastqs', and '/path/to/transcriptome_ref' with actual values.
   # The '--transcriptome' argument should point to the directory created by 'cellranger mkref'.
   cellranger count \
       --id=sample_id_output \
       --transcriptome=/path/to/cellranger_ref/GRCh38_v8.0.0 \
       --fastqs=/path/to/fastqs \
       --sample=sample_id \
       --localcores=16 \
       --localmem=64
   

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