To download 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM v1.1)

data available on the 10x Genomics website here: https://support.10xgenomics.com/single-cell-atac/datasets/1.2.0/atac_pbmc_5k_nextgem

Load packages

To select a feature space

To build a count matrix using scATAC-seq data, it is important to choose a feature space on which to build the count matrix.

epiScanpy offers to load different set of custom features (bed, gtf and gff input files accepted), or to load peaks called using macs2 (see below on how to call peaks). Alternatively, epiScanpy can also generate windows of a given size.

Loading annotation files

Calling peaks

generating windows

Now, to build the count matrix

In this example we are using the peak features and only 2 threads. For a faster result, you should consider using more threads.

Let's now build the geneactivity matrix