SirKuikka

I have the same problem. The first dataset finished succesfully in ~2 hours. ``` Processed 1,000,000 reads in 15.72 seconds. Total reads: 93,000,000 in child 42921 Processed 1,000,000 reads in...

Hi, I have this same problem, and I noticed that the predicted regulon names change a lot depending on how the data are concatenated. In the sc Best Practices [book](https://www.sc-best-practices.org/mechanisms/gene_regulatory_networks.html)...

Plus there's a warning like this miniconda3/envs/squidpy/lib/python3.10/site-packages/spatialdata_io/_utils.py:48: UserWarning: The "cell_id" column in the cells metadata table does not match the "cell_id" column in the annotation table. This could be due...

@philinscience No, but Seurat doesn't have this issue.

At least I noticed that the different clusters correspond to different V and J genes, so the distance is heavily driven by those.