Cells vanishing after merging processed .h5ad and spliced/unspliced matrix (also .h5ad)
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I am using scanpy and python to process single cells data.
I am trying to run an RNA velocity analysis with scvelo, after merging my processed data and my spliced/unspliced matrix using :
merged_scv_adata = scv.utils.merge(processed_adata, ad_splice, copy=True)
A lot of cells are vanishing, especially from one cluster in particlular, is it normal ? How could I correct that ?
print('Processed : \n',cluster_counts)
Processed :
integrated_cluster
0 5037
1 4958
2 3469
3 2568
4 989
5 707
6 650
7 525
cluster_counts = merged_scv_adata.obs['integrated_cluster'].value_counts()
print('Merged : \n', cluster_counts)
Merged :
integrated_cluster
0 4707
1 4488
3 2367
4 911
6 643
5 630
2 607
7 492
Please check existing and related issues.