Hi!

I'm currently using ArchR for a scATAC-seq analysis. I'd like to get BAM files after batch correction using "Harmony" in ArchR. Namely, a bam file for each cluster in each sample.

I would appreciate any help.

# after reading inputFiles (2 inputFiles from 2 samples)
ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  minTSS = 6, 
  minFrags = 2000, 
  maxFrags = 1e+05,
  addTileMat = TRUE,
  addGeneScoreMat = TRUE, force=T
)
doubScores <- addDoubletScores(
  input = ArrowFiles,
  k = 10, 
  knnMethod = "UMAP", 
  LSIMethod = 1
)
proj <- ArchRProject(
  ArrowFiles = ArrowFiles, 
  outputDirectory = "HemeTutorial",
  copyArrows = TRUE 
)
getAvailableMatrices(proj)
proj <- filterDoublets(ArchRProj = proj, filterRatio = 2.5)
proj <- addIterativeLSI(ArchRProj = proj, useMatrix = "TileMatrix", name = "IterativeLSI")
proj <- addHarmony(
  ArchRProj = proj,
  reducedDims = "IterativeLSI",
  name = "Harmony",
  groupBy = "Sample"
)
proj <- addClusters(input = proj, reducedDims = "Harmony")