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In my last post, I showed you how to use PCA for bulk RNAseq data.
Today, let’s see how we can use it for scATACseq data.
Download the example dataset from 10x genomics
https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_pbmc_5k_v1
The dataset is 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v1.0).
Download the atac_pbmc_5k_v1_filtered_peak_bc_matrix.tar.gz file and unzip it.