Looking for a bit of guidance,
I’m working with a tabular count matrix, for single cell RNA seq. I had come across issues when I was attempting to filter the data, RaceID filters the data, but removes large numbers of cells, so I was exploring other tools. Most of the tools required me to change the file type, from a tabular matrix, to either a Loom, AnnData or H5ad. I changed the files to H5ad types, and successfully filtered the data using scanpy. However, now that I am trying to plot the data, its seems that no tool I can find will plot a PCA or t-SNE at all. I’ve tried changing file types again but still nothing works. Just wondering if you had any advice on this? Is changing the file type too much affecting the data?
Included is a screenshot of the final file type I am trying to plot, which again no tool will plot.