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Help with the error: Cannot find assay integrated

Hi all,

Could we use the same pipeline to analyze single cell RNA seq for single cell nuclei RNA seq? I got this error but could not find the reason on the Internet:

DefaultAssay(merged_seurat) <- "integrated"

Error in `DefaultAssay<-.Seurat`(`*tmp*`, value = "integrated") : 
  Cannot find assay integrated

Would you please have a suggestion? Thank you so much!

seurat
• 1,824 views • link
written by Chris • Chris

Please check the available assays in your merged_seurat. There is no integrated assay present that's why Seurat is giving you an error message. You can check available assays in a Seurat object as follows-

# Check available assays
available_assays <- Assays(merged_seurat)

# Print the list of available assays
print(available_assays)

Yes, you can basically use the same pipeline to analyze single cell nuclei RNAseq data. However, you should be cautions in removing ambient RNA contamination processes.

• 0 views • link
written by bk11 • bk11

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