Question: Can I generate a matrix h5 file from a molecule_info.h5 file?
Answer: Yes, the molecule_info.h5 file contains all molecule information and can be used to re-generate the gene-barcode matrix files.
Although the main purpose of the cellranger aggr pipeline is to combine multiple 10x libraries in a single analysis, it could also be used to analyze data from a single library with a molecule_info.h5 file.
You would provide the path to the molecule info file in the CSV input file for cellranger aggr:
library_id,molecule_h5
LV123,/opt/runs/LV123/outs/molecule_info.h5
The pipeline will generate the matrix h5 files, .cloupe file and the web summary HTML file.