Build count table from FASTQ reads and a list of selected kmers

Build count table from FASTQ reads and a list of selected kmers

Usage

BascetQueryFq(
  bascetRoot,
  inputName = "filtered",
  outputName = "kmer_counts",
  useKMERs,
  maxReads = 1e+06,
  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

useKMERs

List of KMERs to query

maxReads

The maximum number of reads per cell to sample

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 to be executed, or being executed, depending on runner settings