Topic
Doublets
Which of my clusters are two cells in one droplet?
At typical 10x loading, 5-10% of droplets contain two cells. Heterotypic doublets form clusters that look like transitional states and express markers of two lineages; homotypic doublets inflate counts and are nearly invisible.
- How to Find and Remove Doublets in Single-Cell ATAC-seq
A cluster that looks like a transitional cell state is often two nuclei in one droplet, and scATAC-seq doublets need fragment-based tools, not the scRNA-seq playbook.
- How to Find and Remove Doublets in Single-Cell RNA-seq
A bridge cluster co-expressing two lineage markers is not a transitional cell state until you've ruled out that it's two cells sharing one droplet.
- How to Find and Remove Doublets in Single-Nucleus RNA-seq
A cluster that co-expresses two lineage markers isn't always a transitional cell state, and the fix depends on telling homotypic from heterotypic doublets before you delete anything.