Help with the error: Cannot find assay integrated

Question

[Chris]

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!

[bk11]

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.

[Chris]

Got it. Thank you so much! I follow this: https://satijalab.org/seurat/articles/integration_introduction

that why I use "integrated". Don't know why I only have 'RNA' as available assays