Merge Gene expression and Antibody capture data in Seurat

Question

[chi.delta]

Hey everyone,

I am currently analyzing some mouse 10x scRNA seq data ( after the mapping with cellranger I got 3 output files: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz) I was able to read my data:

my_counts<-Read10X(data.dir = "data")

I then tried to create a Seurat object:

seu <- CreateSeuratObject(counts = my_counts, min.cells = 3, min.features = 200) But I get the following error:

Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features) : No cell names (colnames) names present in the input matrix

I next tried to create one Seurat object for each type of data (rna vs protein)

seurat_gex = CreateSeuratObject(counts = my_counts$Gene Expression, min.cells = 3, min.features = 200, project = "eae14")

seurat_cite = CreateSeuratObject(counts = my_counts$Antibody Capture)

This worked fine. I could then go on with the seurat_gex object for further filtering etc.

Is there a way to import the antibody data into my rna data object?

Thanks

Answer 1

[Kevin Blighe]

I was recently working with this dataset. If you remove the third column in features.tsv.gz, Seurat will just import everything together. There may be other [as yet unknown to me] functionality in Seurat to do this, though

[chi.delta]

Great thanks, this worked. I also found out that one can use the following to add the colnames and rownames :)

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices