Issue with CreateSeuratObject about simpli HOT 6 CLOSED

Thank you so much Michele! It works now.

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Hi Alessia,

Could you share the input files: "annotated_cells.csv", "sample_metadata_SEN.csv"? I suspect there could be some issue with the way the script is reading the "CellName" column of the "annotated_cells.csv" file. Does it contain any special characters?

Best,

Michele

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Hi Michele,

thanks for quick reply!
You can download the input files from the link below.
Archive.zip

The CellName is generally something like this:Alz_A16317_EC_2-1 so no special characthers unless too many underscores is an issue.

Thanks a lot for your help!

Best
Alessia

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Perfect, thank you for the files. I had a very quick look and all the names seem fine, underscores should be totally OK. I will try running the script in the singularity container and see if I get the same error. I'll update you when I reproduce the error.

Best

Michele

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Thanks a lot Michele!

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OK, so the error is caused by one of the samples ("Ctrl_PDC16_MTG_4") having only one cell in the "all_cells". You can find a fix in: #10. It is not merged yet, but you can just switch to this branch for the fixed code. or just download the script from here. Now it works for me with your script, but please let usknow if you find any issues downstream.

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