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Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
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CITE-seq data filtering #17

Open BMBlobner opened 2 years ago

BMBlobner commented 2 years ago

Were any steps taken to filter the background noise from unbound antibody from the CITE-seq data?

gAleryani commented 2 years ago

Hi @BMBlobner, my apologies for the late reply, I was away. We did not filter for background noise. We tried a number of approaches however found suboptimal performance without the appropriate controls, needs something beyond that of IgG isotype controls. How best to do so is probably the biggest challenge in the analysis of CITE-seq data at the moment!