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HuBMAP Use Case Library.
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Accessing Cell X Genes Files Without MAGIC Smooth #12

Closed bhonick closed 7 months ago

bhonick commented 1 year ago

A user submitted the following inquiry to the HuBMAP Helpdesk:

I think that for the atac seq data (like https://portal.hubmapconsortium.org/browse/dataset/d2a5974f9fbc2d489970b199ee007578 https://portal.hubmapconsortium.org/browse/dataset/d2a5974f9fbc2d489970b199ee007578 ), I can only access cell x bin and cell x gene files, for the later file (cell x gene), the matrix is smoothed by magic. This is a quite large file, and I wonder if I can access the cell x genes file without magic smooth or not. Since the file has been changed to cell x bin, it will be quite hard for me to use Seurat to calculate the gene activity score again.

The following tags are applicable: Explore HuBMAP Data Experimental Biologist Computational Biologist Clinician Data Contributor Educator Student

tsliaw commented 7 months ago

This is now captured as a user request in the internal HIVE-HMS Jira as this does not reflect a high level use case and more of a user request.