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marker genes not specific for cluster after imputation #27

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yamihn opened this issue Dec 5, 2023 · 0 comments
Open

marker genes not specific for cluster after imputation #27

yamihn opened this issue Dec 5, 2023 · 0 comments

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@yamihn
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yamihn commented Dec 5, 2023

hi, I imputed my dataset with alra in seurat. after the imputation I integrated the alra assay and calculated pca, umap and clusters. the problem is that when I look for the top markers per cluster, using alra as an assay, I don't find anything specific for that cluster. should I use the rna assay? or what is the problem?
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