Sample-wise raw count matrix from 10x multiplexed data

Question

[AB]

Hi all,

I want to run SoupX on my mulitplexed single cell RNASeq data. Now, 10X gives per sample counts for the filtered data but the raw data for all the samples are combined into one big file in the raw_feature_bc_matrix folder. I figured I should be able to separate the raw counts per sample by using the hashing info or the sample_molecule_info.h5 file, but I cant find the hashing info when I read in the raw_feature_bc_matrix.h5 or the raw_feature_bc_matrix.h5 files and the sample_molecule_info.h5 file in the per_sample_outs directory still has all the barcodes for all samples combined. Is there is a good way to get per sample raw counts from the 10x output ?

[kkohl]

I've exactly the same problem and wanted to ask whether you found a solution that you would be willing to share? Did you do it via per sample raw counts or merged filtered counts? Or is there any other solution to it?