ArchR vs Signac for calculating number of fragments per sample (nFrags)

[tangybat]

Hi,

I have noticed during quality control of my atac-seq data that one of my samples, sample #4, has an abnormally low number of fragments in ArchR but not in Signac. Is there a difference between how ArchR and Signac calculates the number of fragments for each sample? How does Signac calculate this value?

The ATAC_Fragments information came from the cellranger-arc count pipeline, which I added in as metadata.
https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/per_barcode_metrics

Both ATAC_Fragments (Signac) and nFrags (ArchR) should represent unique nuclear fragments.

Signac:
VlnPlot(object = comb, features = c('ATAC_Fragments'), group.by = 'orig.ident',pt.size = 0,ncol=2, log=T)

ArchR:

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  filterTSS = 4,
  filterFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)
proj <- ArchRProject(
  ArrowFiles = ArrowFiles, 
  outputDirectory = "PBMC",
  copyArrows = FALSE #This is recommended so that you maintain an unaltered copy for later usage.
)
plotGroups(
  ArchRProj = proj, 
  groupBy = "Sample", 
  colorBy = "cellColData", 
  name = "log10(nFrags)",
  plotAs = "violin",
  alpha = 0.4,
  addBoxPlot = TRUE
)

[rcorces]

The number of fragments shown on the ArchR plot represents the data from cells that have passed your filters. If your Signac and ArchR plots represent different subsets of cells because of different ways that the two tools define a pass-filter cell, then this result is not surprising. Generally speaking, cells with low-TSS enrichment can have very large numbers of fragments.