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What do you do if you have multiple samples
If you have multiple samples (multiple cellranger output directories), read each one in and create individual seurat objects. Then, merged them into one object. You may want to use the project parameter to indicate condition information. You can also add metadata to do this.
From Seurat documentionWhen merging, to easily tell which original object any particular cell came from, you can set the add.cell.ids parameter with an c(x, y) vector, which will prepend the given identifier to the beginning of each cell name. The original project ID will remain stored in object meta data under orig.ident.
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data10<-Read10X(data.dir = "../../10/outs/filtered_feature_bc_matrix")
pbmc10<-CreateSeuratObject(counts = data10, project="dep")
data11<-Read10X(data.dir = "../../11/outs/filtered_feature_bc_matrix")
pbmc11<-CreateSeuratObject(counts = data11, project="control")
data14<-Read10X(data.dir = "../../14/outs/filtered_feature_bc_matrix")
pbmc14<-CreateSeuratObject(counts = data14, project="dep")
data16<-Read10X(data.dir = "../../16/outs/filtered_feature_bc_matrix")
pbmc16<-CreateSeuratObject(counts = data16, project="control")
pbmc.combined<-merge(pbmc10, y=c(pbmc11,pbmc14,pbmc16),add.cell.ids = c("10","11","14","16), project = "pbmc", merge.data = TRUE) |
Single Cell Proportion Test
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