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aertslab / SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
GNU General Public License v3.0
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ValueError: Intersection of gene_names and tf_names is empty. #47

Closed agarmill closed 3 years ago

agarmill commented 3 years ago

Hello,

Thank you for this resource! I am running the PBMC10k_SCENIC-protocol-CLI.ipynb protocol, and when I run SCENIC Steps phase 1a, I get an error.

!pyscenic grn {f_loom_path_scenic} {f_tfs} -o adj.csv --num_workers 20 ValueError: Intersection of gene_names and tf_names is empty.

I have tried transposing the original matrix (as as is suggested in another issues post) but I still get the same error. Is there another reason I could be getting this error?

Thank you!

cflerin commented 3 years ago 
Intersection of gene_names and tf_names is empty

A common cause is for this is using different gene symbols for the TFs vs expression matrix. This is what I would check first (along with possibly transposing the expr matrix).