Clustering artefacts when processing single-nucleus RNAseq
I've been downloading and processing publicly available 10x genomics single-cell data.
But I've been having a particularly hard time with a single-nuclei AD dataset (GSE174367).
Specifically, in addition to cell-type specific clustering I am seeing hundreds of tiny clusters.
I've tried setting the expected doublet rate higher than normal when removing doublets, as well as implementing stricter QC
filtering thresholds, but they remain...
Even at high cluster resolutions the smaller clusters are often grouped with the larger ones.
Has anyone seen this type of artefact before?
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