For performing sample similarity tSNE, highly correlated motifs or kmers as well as motifs or kmers with variability below a certain threshold (1.5) were first removed from the bias corrected deviations matrix. The transpose of that matrix was then used as input to the Rtsne package28, with a perplexity parameter of 8 used for the down-sampled bulk hematopoiesis data and 25 for the single cell ATAC-seq data.
