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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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'list' object has no attribute 'intersection' #235

Open lemonsky123 opened 5 months ago

lemonsky123 commented 5 months ago

Hi, @kaizhang . Thanks for developing SnapATAC2. When I was running the anndata.concat function in the "Annotating cell clusters by integrating single-cell RNA-seq data" tutorial, an error occurred "AttributeError: 'list' object has no attribute 'intersection'" U 6NZEN9UYHE60 1AV61(UD the "reference" data was generated by Scanpy and scVI, the query was generated by SnapATAC2. They are shown below image

Could you help me solve this problem? Thanks very much. Best

kaizhang commented 5 months ago

You are using the concat function from the anndata package. Please make sure the AnnData objects are read by the read function from the anndata package (or in in-memory mode).

lemonsky123 commented 4 months ago

You are using the concat function from the anndata package. Please make sure the AnnData objects are read by the read function from the anndata package (or in in-memory mode).

Hi, thanks very much for your prompt reply. @kaizhang . The reference object is imported by snap.read, and the query object is generated by snap.pp.make_gene_matrix, which is show below image image I just followed the tutorial ""Annotating cell clusters by integrating single-cell RNA-seq data" step by step.