Running too-many-cells with normalized data

Question

Running too-many-cells with normalized data

ghoshal opened this issue 6 years ago · 3 comments

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

Answer 1 · 2019-04-11T12:45:11.000Z

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.

Answer 2 · 2019-04-11T14:26:11.000Z

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.

Answer 3 · 2019-04-11T14:51:55.000Z

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.