Index a genome using STAR such that it can be used for alignment

Index a genome using STAR such that it can be used for alignment

Usage

BascetIndexGenomeSTAR(
  fastaFile,
  gtfFile,
  outDir,
  numLocalThreads = NULL,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

fastaFile

Name of FASTA file holding genome sequence

gtfFile

GFF file holding genome annotation

outDir

A directory in which to store the index. This directory will be created

numLocalThreads

The number of threads to use for the STAR index, for each runner. Default is the maximum, taken from runner settings

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