To profile the time required for an end-to-end analysis of each dataset starting from the raw data (the fragment file) and a set of peaks, we ran CreateFragmentObject, CreateChromatinAssay and CreateSeuratObject to create the objects in R required for an analysis, followed by FeatureMatrix for quantification, NucleosomeSignal and TSSEnrichment for QC, FindTopFeatures, RunTFIDF, RunSVD and RunUMAP for dimension reduction and FindNeighbors and FindClusters for cell clustering. This was performed using eight cores by setting plan(‘multiprocess’, workers = 8) using the future R package (https://cran.r-project.org/package=future).
