Loss of 'var' using concatenation of AnnData objects

Question

[Rachel]

Hello all! I am doing scRNAseq analysis in python using scanpy library and am having multiple different issues during concatenation of my 16 samples (stored previously in adata_list).

The following line of code results in a loss of genes (n_vars):

adataConcat = sc.concat(adata_list, merge='same')

Output:

AnnData object with n_obs × n_vars = 111386 × 13620
    obs: 'n_genes'
    var: 'gene_ids', 'feature_types', 'genome'

While running this line of code results in a loss of var data ('gene_ids', 'feature_types', 'genome'):

adataConcat = sc.concat(adata_list, join='outer', merge='same')

Output:

AnnData object with n_obs × n_vars = 111386 × 15702
    obs: 'n_genes'

How do I retain both during a concatenation?

Answer 1

[Hugo]

Similar question has been asked and answered on scverse discourse