scv.utils.merge show less number of Cell barcode and change obs_names

Hi,

I have two samples data sets and ran velocyto each. I am trying to use scv.utils.merge(1st_adata, 2nd_adata) to merge two data sets. After scv.utils.merge, less number of cells and changed obs_names as well. It seems n_vars are kept while n_obs is changed. Is there any way to merge two sets without loss? (e.g. 1st set = (n_obs × n_vars = 9206 × 55421), 2nd set = (n_obs × n_vars = 8941 × 55421), merged set = (n_obs × n_vars = 18147 × 55421))

1st data

adata AnnData object with n_obs × n_vars = 9206 × 55421 var: ‘Accession’, ‘Chromosome’, ‘End’, ‘Start’, ‘Strand’ layers: ‘ambiguous’, ‘matrix’, ‘spliced’, ‘unspliced’

adata.obs_names Index([‘possorted_genome_bam_T851Q:AAACCCAAGGCTCTAT’, ‘possorted_genome_bam_T851Q:AAACCCAAGTGACACG’, … ‘possorted_genome_bam_T851Q:TTTGTTGTCGAACGCC’], dtype=‘object’, length=9206)`

2nd data

adata_2 AnnData object with n_obs × n_vars = 8941 × 55421 var: ‘Accession’, ‘Chromosome’, ‘End’, ‘Start’, ‘Strand’ layers: ‘ambiguous’, ‘matrix’, ‘spliced’, ‘unspliced’

adata_2.obs_names Index([‘possorted_genome_bam_OB274:AAACCCAGTAGTCTGT’, ‘possorted_genome_bam_OB274:AAACCCAGTCGGCACT’, … ‘possorted_genome_bam_OB274:TTTGTTGTCTCGCTCA’], dtype=‘object’, length=8941)’

merge two AnnData

merged_adata = scv.utils.merge(adata, adata_2) merged_adata AnnData object with n_obs × n_vars = 31 × 55421 obs: ‘initial_size_unspliced’, ‘initial_size_spliced’, ‘initial_size’ var: ‘Accession’, ‘Chromosome’, ‘End’, ‘Start’, ‘Strand’ layers: ‘ambiguous’, ‘matrix’, ‘spliced’, ‘unspliced’’

check 2nd data obs names again

adata_2.obs_names Index([‘AAACCCAGTAGTCTGT’, ‘AAACCCAGTCGGCACT’, ‘AAACCCAGTTAGGCTT’, … ‘TTTGTTGTCTCGCTCA’], dtype=‘object’, length=8941)’

[VolkerBergen]

In that case, you wouldn’t want to merge but to concatenate the two datasets, which can be done with adata = adata1.concatenate(adata2).

[VolkerBergen]

Great to hear, that it got resolved. Will need to add some informative warning in anndata.concatenate.