tSNE and UMAP of scATAC-seq data looks like spaghetti

tSNE and UMAP of scATAC-seq data looks like spaghetti

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I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment.

I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I get.

I tried multiple perplexities from 5 to 50, number of components from 20 to 200, and UMAP. However the results were roughly the same.

Do you know what could cause this? I did not filter out peaks before running this because I am not sure what cutoff to use.


cell


single


umap


tsne


ATAC

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