Cell cluster that mainly consists of doublet.
Hi! After I used DoubletFinder to detect doublets in my dataset, I found out that some clusters have a really high percentage of doublets, for example, over 50%. Should I remove those clusters entirely since all the cells in those clusters might be doublets, or should I just remove the cells that are detected as doublets?
• 1,100 views
•
link
updated
by
jared.andrews07
•
written
by
D •
•
written
by
D •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Doublet Detection in SMART-Seq2 single-cell data
written by luca8650 •
-
How to handle a scattered cluster with mixed cell type markers in scRNA-seq subclustering analysis?
written by maplewj •
-
Doublet Detection for Intestinal Immune Cells in scRNA-seq
written by s •
-
Can I use a dataset that has batch effect as a reference in scmap?
written by D •
-
Doublets in scRNAseq analysis
written by Binghong •
-
Do I need to remove doublets after before or after running hashsolo?
written by bioinfo •
-
High number of detected genes per cell after doublet removal - scRNAseq data
written by sarahmanderni
-
Filter out doublet and Clustering
written by synat.keam •
-
Forum: Steps after doublet detection in single cell data
written by ishwarvh •
-
Removing overrepresented sequences in paired end RNA-seq
written by LayneSadler
Look at nCount_RNA of cells in that cluster. Does it appear to be significantly higher across the entire cluster? Typically normalisation and scaling before clustering tries to correct differences due to depth/counts so it isn't a given that all the doublets will cluster together.
In addition, look at the markers for that cluster. Do they contain clear indications of 2 (or more) different cell types? If so, probably safe to remove.
However, on occasion, some of the doublet-finding algorithms can label legitimate transitory populations as doublets, so it's worth taking a closer look at them.