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Clustering artefacts when processing single-nucleus RNAseq

Hello,

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.

enter image description here

Has anyone seen this type of artefact before?

single-cell rna seurat umap
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written by MikeV • MikeV

what tools produces this plot? sometimes the number of clusters is specified as an external parameter

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written by Istvan Albert Istvan Albert

This is using the harmony + Seurat workflow.

o <- Seurat::RunUMAP(o,reduction = "harmony", dims = 1:30)
o <- Seurat::FindNeighbors(o,reduction = "harmony", dims = 1:30)
o <- Seurat::FindClusters(o,resolution = 0.1)

You're right though, I haven't tried tinkering with UMAP/clustering settings. Will give that a go.

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written by MikeV • MikeV

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