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hbctraining / scRNA-seq_online

https://hbctraining.github.io/scRNA-seq_online/.
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v5 issue with GetAssay() #114

Closed mistrm82 closed 1 month ago

mistrm82 commented 7 months ago

Once you have run:


# 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))

You will need to use the JoinLayers():

filtered_seurat <- JoinLayers(filtered_seurat) Now when you run GetAssayData, it should work without an error:

# Extract counts
counts <- GetAssayData(object = filtered_seurat, slot = "counts")
mistrm82 commented 1 month ago

this has been added to 03 after merging samples into a single object