Splitting single cell data

Question

[otieno43]

I merged single cell RNA seq data but now I want to separate them. how do I do this? Below is what I did..

sce.rep1 <- read10xCounts(fname, col.names=TRUE)
sce.rep2 <- read10xCounts(fname1, col.names=TRUE)

I the combined the two

All_scell <- list(sce.rep1, sce.rep2)

I then order the data

All_scell <- mget(ls(pattern = "^sce.rep[0-9]"))

Removed rRNA

rRNA_Scell <- import.gff3("/Users/TrypDB.gff") %>% 
as_tibble() %>%
filter(type=="rRNA") %>%
select(ID, description) %>%
mutate(ID = gsub("\\.1", "", ID))
for (i in 1:length(All_scell)) {
All_scell[[i]] <- All_scell[[i]][!rownames(All_scell[[i]])%in%rRNA_Scell$ID,]}

Removed empty cells

set.seed(123456)
All_scell <- lapply(All_scell, function(x){
    e.out <- emptyDrops(counts(x), lower = 1000)
    x <- x[ ,which(e.out$FDR<=0.001)]})

Now I want to separate the filtered two datasets (sce.rep1 , sce.rep2) as a seurat object. some help please, thanks.