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