Merge seurat object

[dongmin7591]

I recently updated to seurat v5. Previously, when version 4.3 was used, the merged seurat object created after merging was divided into one layers (counts, data), but in seurat 5, counts.1,2,3,... or data1,2,3,... depending on the number of each sample. Why is expression data not merged? Is there another way?

[Dooo0k]

Use the JoinLayers() function to merge multiple layers into a single layer.
ex) obj <- JoinLayers(obj)

[alekseybelikov]

this function doesn't work. I still have separate layers after using it

[alekseybelikov]

merged_seurat_2 <- JoinLayers(
  object = merged_seurat,
  layers = c(
    "counts.Sample19M_RT00375N",
    "counts.Sample29M_RT00376N",
    "counts.Sample40M_RT00391N",
    "counts.Sample41M_RT00377N",
    "counts.Sample44M1_RT00383N",
    "counts.Sample44M2_RT00388N",
    "counts.Sample45M_RT00374N",
    "counts.Sample47M_RT00373N",
    "counts.Sample52M_RT00387N",
    "counts.Sample60M_RT00382N",
    "counts.Sample66M_RT00384N",
    "counts.Sample79M_RT00378N"
  )
)

Layers(merged_seurat_2)

'counts.Sample19M_RT00375N''counts.Sample29M_RT00376N''counts.Sample40M_RT00391N''counts.Sample41M_RT00377N''counts.Sample44M1_RT00383N''counts.Sample44M2_RT00388N''counts.Sample45M_RT00374N''counts.Sample47M_RT00373N''counts.Sample52M_RT00387N''counts.Sample60M_RT00382N''counts.Sample66M_RT00384N''counts.Sample79M_RT00378N'