Setting up a test run

sinclair run --mode slurm -profile test

About the data

FILE: WB_Lysis_Granulocytes_3p_Introns_8kCells_fastqs.tar

TYPE: GEX

NAME: Whole Blood RBC Lysis for PBMCs and Neutrophils, Granulocytes, 3'

PRODUCT: Single Cell Gene Expression Dataset by Cell Ranger 6.1.0

INFO:

Donor Information: healthy female.

Isolation protocol: CG000392 RevA: Isolation of Leukocytes, Bone Marrow and Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing - Whole Blood Lysis for Granuloctyes track.

Whole transcriptome/Gene Expression libraries were generated as described in the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000204 Rev D).

TUTORIAL: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/tutorials/neutrophils

SOURCE: https://www.10xgenomics.com/resources/datasets/whole-blood-rbc-lysis-for-pbmcs-neutrophils-granulocytes-3-3-1-standard

Sample set up and files

WB_1

  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_I1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_I2_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_R1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_R2_001.fastq.gz

WB_2

  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_I1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_I2_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_R1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_R2_001.fastq.gz

WB_3 and WB_4 are copies

  • WB_1 → WB_3
  • WB_2 → WB_4

samples were then subsampled with a set seed

  • WB_1 → sample1,sample2 → s100
  • WB_2 → sample3,sample4 → s101
  • WB_3 → sample5,sample6 → s102
  • WB_4 → sample7,sample8 → s103

grouping tests should be

for single sample

  • group1

for multiple samples

  • group1,group2
  • group1,group2,group3