Hello!
I’m having trouble reading my .h5 files to a 10x mm10 Custom Genome containing LacZ. When I run this file in Seurat it picks up the LacZ gene but in scanpy the gene seems to be missing. I tried to run the convert seurat object and got this error:
CtrlSeuratObj.h5ad’ contains more than one genome. For legacy 10x h5 files you must specify the genome if more than one is present. Available genomes are: [‘X’, ‘obs’, ‘obsm’, ‘raw’, ‘var’, ‘varm’]
How can I insert my custom genome into the sc.read_10x_h5 function so that I can detect the LacZ gene?
thanks in advance!