pyscenic grn: error: argument expression_mtx_fname

aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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pyscenic grn: error: argument expression_mtx_fname #585

Open yulchen810 opened 2 days ago

yulchen810 commented 2 days ago

[This has been resolved by removing quote] Hi, Thank you for your excellent work. I'm running pyscenic using docker hub. I can open the expressionMatrix in vs code, but it reports an error pyscenic.cli.pyscenic - ERROR - The expression matrix supplied does not contain any genes. Make sure the extension of the file matches the format (tab separation for TSV and comma sepatration for CSV).

Could you please have a look at this issue? Thank you very much!

ghuls commented 2 days ago

To me it looks like your expression matrix does not contain TABs but spaces as separators.

awk -v OFS='\t' '$1 = $1' /d/pyscenic/data/FB6_countsMatrix.tsv > /d/pyscenic/data/FB6_countsMatrix.with_tabs.tsv