3a. Set paths to project files

PROJECT_DIR <- "$HOME/cellranger_output/"

E12_fragments_path <- file.path(PROJECT_DIR,
    "scATAC_E12/outs/fragments.tsv.gz")
E18_fragments_path <- file.path(PROJECT_DIR,
    "scATAC_E18/outs/fragments.tsv.gz")
P5_fragments_path  <- file.path(PROJECT_DIR,
    "scATAC_P5/outs/fragments.tsv.gz")
P30_fragments_path <- file.path(PROJECT_DIR,
    "scATAC_P30/outs/fragments.tsv.gz")
inputFiles <- c(E12_fragments_path,
                E18_fragments_path,
                P5_fragments_path,
                P30_fragments_path)
names(inputFiles) <- c("E12", "E18", "P5", "P30")

3b. Generate arrow files

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  minTSS = 4, # Don't set this too high initially because you can increase later
  minFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)