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10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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ArchR vs Signac for calculating number of fragments per sample (nFrags) #191

Closed tangybat closed 8 months ago

tangybat commented 1 year ago

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)

nFrags_Signac_erasedsamples

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
)
nFrags_ArchR