Cellcyclescoring did not work in Seurat V5

Question

[synat.keam]

Dear All,

Not sure anyone has come across issue with cell cycle scoring in seurat recently.

data.filt<- NormalizeData(data.filt)

#Cell cycle  
data.filt<- CellCycleScoring(object = data.filt, g2m.features = cc.genes$g2m.genes, 
                             s.features = cc.genes$s.genes)

# Error I got

Error in `GetAssayData()`:
! GetAssayData doesn't work for multiple layers in v5 assay.
Backtrace:
 1. Seurat::CellCycleScoring(...)
 2. Seurat::AddModuleScore(...)
 4. SeuratObject:::GetAssayData.Seurat(...)
 6. SeuratObject:::GetAssayData.StdAssay(object = object[[assay]], layer = layer)
Error in GetAssayData(object = object[[assay]], layer = layer) :

Some people have encountered the same issues, but I did not see any solution that worked for me yet. Anyone know how to fix this, i really appreciated.

Kind Regards,
Synat

[fracarb8]

You can try to merge the layer together with data.filt <- JoinLayers(data.filt)

[bk11]

This vignette will help you. https://satijalab.org/seurat/articles/seurat5_cell_cycle_vignette

[wanaga3166]

Sorry, but this link doesn't work.

[Bastien Hervé]

https://satijalab.org/seurat/articles/cell_cycle_vignette