/snakemake-scrnaseq

Basic snakemake pipeline to process and analyze single-cell datasets

snakemake-scrnaseq

About the dataset

In this mini-project, a single-cell RNA-Seq dataset will be processed and analyzed in a simple snakemake pipeline.

This dataset comes from the "1k PBMCs from a Healthy Donor using v3 chemistry" dataset by 10x and processed by Cell Ranger 3.0.0. The stats of this dataset are:

  • 1,222 cells detected
  • Sequenced on Illumina NovaSeq with approximately 54,000 reads per cell
  • 28bp read1 (16bp Chromium barcode and 12bp UMI), 91bp read2 (transcript), and 8bp I7 sample barcode
  • run with --expect-cells=1000

Single-cell RNA-Seq snakemake pipeline

This is how I processed the data...