I’m reading in a text file, however adata.obs and adata.vars have no categories like gene ids. How would I go about adding this?
You can define your anndata obs and var indices by using:
adata.obs_names = ... adata.var_names = ...
Are the observation names and var names present in your text file ?
Could you give a subset of your text file (like 5 first lines and rows) ?