Var counts 0 after gene filtering

Help anndata
1

Hello,

I am pretty new to scanpy so it is probably a simple question. When I try to read data downloaded from GEO: GSE217930 . All my adata.var have the same gene_ids and when I try to filter genes I get n_vars=0. How could I fix this problem?

adata = sc.read_10x_mtx(‘…/input/079 adult1 day0/’)
adata

UserWarning: Variable names are not unique. To make them unique, call .var_names_make_unique.
utils.warn_names_duplicates(“var”)
AnnData object with n_obs × n_vars = 3583 × 33538
var: ‘gene_ids’, ‘feature_types’

adata.obs

AAACCCACAACCAATC-1
AAACCCACACGGATCC-1
AAACCCACACTTCATT-1
AAACCCACAGAGACTG-1
AAACCCAGTCTTCAAG-1
…
TTTGTTGTCCCAATAG-1
TTTGTTGTCGGTAACT-1
TTTGTTGTCGTGCTCT-1
TTTGTTGTCTAGTCAG-1
TTTGTTGTCTGGTTGA-1

adata.var

gene_ids	feature_types

FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
… … …
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression
FAM138A ENSG00000237613 Gene Expression

sc.pp.filter_genes(adata, min_cells = 10)

adata

AnnData object with n_obs × n_vars = 12105 × 0
var: ‘gene_ids’, ‘feature_types’, ‘n_cells’

2

Solved it. Thank you for the fantastic package keep up the good work!