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Bug report [BUG] cistopic_obj has nan values for sample and leiden column after adding cell_data #168

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yojetsharma opened this issue Sep 17, 2024 · 0 comments

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@yojetsharma
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yojetsharma commented Sep 17, 2024

Describe the bug
I used cell_data from my snRNA seq data (generated independently using the cellranger and not cellranger-arc). This was added to the cis_object that was generated using the atac seq data (generated using the cellranger-arc). The cistopic_obj seemed to have correct mapping of the barcodes but the sample and leiden columns only have NaNs in them:

                                             barcode  sample  leiden  \
GCCTTACTCTAGCTAA-1-d149___d149    GCCTTACTCTAGCTAA-1     NaN     NaN   
GGACTAAAGCCGCTTT-1-d149___d149    GGACTAAAGCCGCTTT-1     NaN     NaN   
GCCCGTTGTAATGACT-1-d149___d149    GCCCGTTGTAATGACT-1     NaN     NaN   
GTGGATGCATAAACCT-1-d149___d149    GTGGATGCATAAACCT-1     NaN     NaN   
GGTCAGGAGGAACACA-1-d149___d149    GGTCAGGAGGAACACA-1     NaN     NaN   
...                                              ...     ...     ...   
TAGTGAGAGGGATTAG-1-ls003___ls003  TAGTGAGAGGGATTAG-1     NaN     NaN   
GGAGCGATCAATTGGC-1-ls003___ls003  GGAGCGATCAATTGGC-1     NaN     NaN   
GATAAAGGTGGGAACA-1-ls003___ls003  GATAAAGGTGGGAACA-1     NaN     NaN   
GGAAGTATCGTGCTTC-1-ls003___ls003  GGAAGTATCGTGCTTC-1     NaN     NaN   
TGAAACTGTGTTTGCT-1-ls003___ls003  TGAAACTGTGTTTGCT-1     NaN     NaN   

Version (please complete the following information):

  • Python:3.11

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