Questions about using gene expression matrix

[HelloWorldLTY]

Hi, I wonder for the input gene expression matrix based on csv format, is it for cell x gene (like anndata) or gene x cell? Thanks.

[juexinwang]

Please check the tutorial, cell * gene, the standard format as other tools

[HelloWorldLTY]

Thanks a lot.

[HelloWorldLTY]

In the tutorial, it seems like:
*_recon.csv: Imputed gene expression matrix. Row as gene, col as cell. First row as gene name, First col as the cell name.
Therefore, I think it should be a gene x cell matrix. I filter 20000 hvgs and my final matrix loses some cells. Is it normal? Thanks.

[juexinwang]

I myself forget it. You can check the code, the preprocessing will filter both genes and cells, you can setup the threshold by yourself