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linnarsson-lab / loompy

Python implementation of the Loom file format - http://loompy.org
BSD 2-Clause "Simplified" License
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Convert older Loom files to newer specification #152

Open chenu opened 3 years ago

chenu commented 3 years ago

Hi All, I am attempting to analyze some loom files with Seurat. The loom file in question is: https://storage.googleapis.com/linnarsson-lab-loom/l1_pons.loom

Those files have a col_edges and not col_graphs which is what the SeuratDisk library needs to convert the loom file.

Is there something within Loompy that I can use to convert the older loom files to the new specifications.

I tried doing loompy.combine and the new file works fine within Seurat, but I'm unclear whether this process is modifying the data in any detrimental way?

Thanks!

slinnarsson commented 2 years ago

That should be the way to do it