tSNE and UMAP of scATAC-seq data looks like spaghetti
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.
• 37 views
Read more here: Source link