Access to antibody sequence information in scirpy anndata object

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1

Hello,
Currently when you read in some antibody data in 10X format (e.g. filtered_contig_annotations.csv) into annData object using the io.read_10x_vdj function, the antibody sequence information (fwr1,fwr1_aa,cdr1,cdr_aa, etc.) seems to be lost. Is there some way of accessing that information that was present in the original 10X input file, but seems to be lost once you read it into the scirpy object?

thanks

2

Hi,

this should be possible by setting

ir.io.read_10x_vdj(..., include_fields=None)

By default, not all fields are included, because of the vast amount of columns this would create in adata.obs. This will not be an issue anymore after the new datastructure (currently under development in Implement scverse datastucture by grst · Pull Request #356 · scverse/scirpy · GitHub) will be rolled out.