scRNA tutorial

 

https://hbctraining.github.io/scRNA-seq_online/lessons/04_SC_quality_control.html

Cell-level filtering (for Human cells?)

Now that we have visualized the various metrics, we can decide on the thresholds to apply which will result in the removal of low quality cells. Often the recommendations mentioned earlier are a rough guideline, and the specific experiment needs to inform the exact thresholds chosen. We will use the following thresholds:

• nUMI > 500
• nGene > 250
• log10GenesPerUMI > 0.8
• mitoRatio < 0.2

# Filter out low quality cells using selected thresholds - these will change with experiment
filtered_seurat <- subset(x = merged_seurat, 
                         subset= (nUMI >= 500) & 
                           (nGene >= 250) & 
                           (log10GenesPerUMI > 0.80) & 
                           (mitoRatio < 0.20))

UMI: 

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1438-9