How is the ad_rna_annotate.h5ad file generated?

[gaoxiangcao]

Hi ,

I’m working with scBasset and wanted to ask how the ad_rna_annotate.h5ad file is generated. Could you briefly explain the main steps, including any preprocessing or annotations, and the tools/scripts involved?

[hy395]

Hi,

The goal of ad_rna_annotate.h5ad is just to show embedding, cell type annotation, and gene expression. My processing is basically:

1. run scvi to get cell embeddings;
2. sc.tl.leiden(resolution=0.5) to get clusters;
3. sc.tl.rank_genes_groups to get top marker genes per cluster;
4. annotation cell type basic on marker genes;

You can also follow scanpy tutorial to process the scRNA data: https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering-2017.html