saves only the variable features

[SofyaMa]

When I do : SaveH5Seurat(merged_seurat, filename = "merged.seurat.h5Seurat",overwrite = T,save_genes= T)
Convert("merged.seurat.h5Seurat", dest = "h5ad",assay = "RNA", overwrite = T) , in Python the object contains only the 2000 variable genes... I would like to have all genes .. what should I do ? thank you so much in advance !

[to-be-so-lonely]

I think you can try

object <- DietSeurat(object = object, counts = T, data = T, scale.data = F, assays = "RNA", dimreducs = c('pca', 'umap', 'harmony'))
object

as explained in #75