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GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.
https://gregoryschwartz.github.io/too-many-cells/
GNU General Public License v3.0
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Running too-many-cells with normalized data #7

Closed ghoshal closed 5 years ago

ghoshal commented 5 years ago

Hi Greg,

I have normalized data from my scRNAseq analysis pipeline that I would like to use with too-many-cells for hierarchical clustering and creating a tree. How can I do that?

Thanks

GregorySchwartz commented 5 years ago

Do you mean what options to use? Because your data is preprocessed, you should supply --no-filter and --normalization NoneNorm in order to bypass the default filtering and normalization that TooManyCells does.

ghoshal commented 5 years ago

Thanks Greg. Also, is there a specific format for the label file? I have cells from two different conditions that I want to plot on the tree.

GregorySchwartz commented 5 years ago

The setup section in the make-tree usage section of the documentation (https://gregoryschwartz.github.io/too-many-cells/) has the required formats for each file.