Topic
QC thresholds
What mitochondrial and count cutoffs should I use, and which cells am I throwing away?
Fixed cutoffs copied from a vignette remove real biology: tumor cells and cardiomyocytes have high mitochondrial fractions, and plasma cells or neutrophils have low counts. Thresholds should be per sample, data-driven (MAD-based) and inspected against what got removed.
- How to Choose Cell QC Thresholds in Single-Cell ATAC-seq
The QC axes that matter in scATAC-seq aren't the ones your scRNA-seq muscle memory reaches for, and a copy-pasted vignette cutoff will quietly delete a real cell population.
- How to Choose Cell QC Thresholds in Single-Cell RNA-seq
The percent.mt < 5 you copied from a PBMC vignette is quietly deleting the tumor cells, cardiomyocytes, or plasma cells you were funded to study.
- How to Choose Cell QC Thresholds in Single-Nucleus RNA-seq
Your snRNA-seq filter probably came from a whole-cell PBMC vignette, and in nuclei a high mito fraction means cytoplasmic contamination, not a dying cell.
- How to Choose Cell QC Thresholds in Spatial Transcriptomics
Copying the 10% mito cutoff from a PBMC tutorial into your tumor Visium slide will quietly delete every high-mitochondrial tumor spot you came to study.