`--gene-names` results in an anndata object where the vars are ENSEMBL IDs

[Lioscro]

@Lioscro to your point, running the following command (using --gene-names) kb count --h5ad -i ~/utilities/kb/index.idx -g ~/utilities/kb/t2g.txt -x 10XV3 -o "${cDNA_seq[i]}_kb_output" --tmp "${cDNA_seq[i]}_tmp" --workflow lamanno -c1 ~/utilities/kb/spliced_t2c.txt -c2 ~/utilities/kb/unspliced_t2c.txt --filter bustools --gene-names -t 40 ${cDNA_seq1[i]} ${cDNA_seq2[i]}

still results in an anndata object where the vars are ENSEMBL IDs

https://github.com/aristoteleo/dynamo-release/issues/285#issuecomment-1052714189 @jmartinrufino What version are you using?

[jmartinrufino]

kb_python 0.27.0

[Lioscro]

Are both your unfiltered matrix (counts_unfiltered/adata.h5ad) and your filtered matrix (counts_filtered/adata.h5ad) not respecting the --gene-names setting?

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[Gavin-Lijy]

Me too