Cell hashing analysis using muon

[urjabhatt]

I am wondering how I can obtain counts of cell hashing barcodes when I load data using muon. Currently, Seurat has HTODemux to assign singlets to each hash BC. I wondering which software to use in the scanpy universe? I came across scanpy.external.pp.hashsolo but it requires cell_hashing_columns, so I am wondering how I can get that information?

[urjabhatt]

For those like me who struggled to figure out how to get counts data for hashing antibodies in .obs, the below link is helpful. This step is necessary for demultiplexing antibody hashed samples by hashsolo program.

How to install solo-sc or use hashsolo from scvi?

Thank you. It worked for my dataset. The semicolon might be a typo. The code is as the following: import scanpy as sc adata=sc.read_10x_h5("filtered_feature_bc_matrix.h5",gex_only=False) htos = list(adata.var[adata.var["feature_types"] == "Multiplexing Capture"].index.unique()) for hto in htos: adata.obs[hto] = adata.X[:,adata.var.index == hto].toarray() import scanpy.external as sce sce.pp.hashsolo(adata, ['hash1', 'hash2', 'hash3','hash4'])

My fastq files were processed through Cellranger 8.0.1 where I provided information on TotalseqB antibody barcodes as well as Hashtag barcodes. That is the reason I had antibody counts in .X layer of my muon data or mdata which I needed to transfer to .obs of filtered_feature_bc_matrix file.

If my understanding is incorrect, please feel free to correct.