Is it possible to run cell ranger clustering using only a gene x cell matrix? Cellranger reanalyze performs clustering but requires a hd5f file. I don't want to run the whole pipeline (including alignment). I was trying to manually generate a hd5f file to input to cellranger reanalyze. Is this possible?

  • $\begingroup$ Hi @guest (nice distinctive username), your question is understandable. I'm not sure whether its possible, but seems reasonable. If you are seeking conversion to h5df, is there any chance you can provide a limited example of the raw matrix output/input? $\endgroup$
    – M__
    Aug 2, 2019 at 7:14

1 Answer 1


The direct answer is yes. If you have never worked with hdf5 you can start here.

But, cellranger outputs several hdf5 files. You can extract the count matrix from the "/outs/filtered_gene_bc_matrices_h5.h5" file.

They provide a lot of information on how to use the hdf5 format so their their documentation is a good place to start.

In addition: you can also load the data into Seurat, monocle or scanpy and follow their tutorials to analyze the data.


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