scATACseq data are very sparse. It is sparser than scRNAseq. To do clustering of scATACseq data, there are some preprocessing steps need to be done.
I want to reproduce what has been done after reading the method section of these two recent scATACseq paper:
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility Darren et.al Cell 2018 Latent Semantic Indexing Cluster Analysis In order to get an initial sense of the relationship between individual cells, we first broke the genome into 5kb windows and then scored each cell for any insertions in these windows, generating a large, sparse, binary matrix of 5kb windows by cells for each tissue.