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pyscenic grn: error: argument expression_mtx_fname #585

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yulchen810 opened this issue Oct 15, 2024 · 1 comment
Open

pyscenic grn: error: argument expression_mtx_fname #585

yulchen810 opened this issue Oct 15, 2024 · 1 comment
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@yulchen810
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yulchen810 commented Oct 15, 2024

[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!
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@yulchen810 yulchen810 added the bug Something isn't working label Oct 15, 2024
@ghuls
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ghuls commented Oct 15, 2024

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

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