Take aligned BAM file and produce Fragments.tsv.gz, compatible with Signac ATAC-seq style analysis

Take aligned BAM file and produce Fragments.tsv.gz, compatible with Signac ATAC-seq style analysis

Usage

BascetBam2Fragments(
  bascetRoot,
  inputName = "aligned",
  outputName = "fragments",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

inputName

Name of input shard

outputName

Name of output shard

overwrite

Force overwriting of existing files. The default is to do nothing files exist

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance

Value

A job, producing a type of Fragments.tsv.gz