GSE133509 Processing Pipeline

Publication

Nature communications (2020) — PMID 31992716

Dataset

Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

1. 1

   alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.1.1)

   Cell Ranger v2.1.1

   $ Bash example

   # Install Cell Ranger (example, adjust path as needed)
   # wget https://cf.10xgenomics.com/releases/cell-exp/cellranger-2.1.1.tar.gz
   # tar -xzf cellranger-2.1.1.tar.gz
   # export PATH=/path/to/cellranger-2.1.1:$PATH
   
   # Define variables for clarity
   FASTQ_INPUT_DIR="/path/to/your/fastq_files" # Directory containing FASTQ files for the sample
   REFERENCE_PATH="/path/to/cellranger_reference/GRCh38_transcriptome" # Placeholder for Cell Ranger-compatible reference transcriptome (e.g., refdata-gex-GRCh38-2020-A)
   SAMPLE_NAME="my_sample" # A unique name for this sample, used for output directory and matching FASTQ files
   
   # Run cellranger count
   cellranger count \
       --id="${SAMPLE_NAME}_count" \
       --transcriptome="${REFERENCE_PATH}" \
       --fastqs="${FASTQ_INPUT_DIR}" \
       --sample="${SAMPLE_NAME}" \
       --localcores=16 \
       --localmem=64

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