How to set up a files from cellranger of two seperate patient in local computer and load to R using for integrate analysis

[synatkeamsk]

Dear Instructor,

I'm very new to single cell. I could do a single sample analysis using Seurat tutorial. However, once it comes to doing integrated analysis of two sample (one control patient/one treated patient), I could not replicate your code in the following found in integration section.

LoadData("ifnb")

# split the dataset into a list of two seurat objects (stim and CTRL)
ifnb.list <- SplitObject(ifnb, split.by = "stim")

# normalize and identify variable features for each dataset independently
ifnb.list <- lapply(X = ifnb.list, FUN = function(x) {
    x <- NormalizeData(x)
    x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})

# select features that are repeatedly variable across datasets for integration
features <- SelectIntegrationFeatures(object.list = ifnb.list)```

Do I need a metadata file for phenotype of treat/control? How to arrange folder/file in local computer as each sample will have barcode.tsv, genes.tsv, and matrix.mtx. I would like to show umap of treat and untreat and see how different they are? I am wondering **_whether you could suggest some code here._** 

For annotation, do I just need to find the differential expressed genes within the cluster and take that gene list to find what cell type represents the cluster? Thank for taking reading my question. I appreciate your help ! 

Regards,

Synat