text: user4986: 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?
  
  user2675: 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.
  
original_text: 4986: <p>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?</p>
   2675: <p>The direct answer is yes. If you have never worked with hdf5 you can start <a href="https://portal.hdfgroup.org/display/HDF5/Introduction+to+HDF5" rel="nofollow noreferrer"> here</a>.</p>
  
  <p>But, cellranger outputs several hdf5 files. You can extract the count matrix from the  "/outs/filtered_gene_bc_matrices_h5.h5" file.</p>
  
  <p>They provide a lot of information on how to use the hdf5 format so their <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices" rel="nofollow noreferrer">their documentation</a> is a good place to start.</p>
  
  <p>In addition: you can also load the data into Seurat, monocle or scanpy and follow their tutorials to analyze the data.</p>
  