Make index for Rbowtie2 — bowtie2_index • CLIPflexR

Make index for Rbowtie2

bowtie2_index(
  genomeFasta,
  outIndex = gsub("\\.fa|\\.fasta|\\.fna", "", genomeFasta),
  overwrite = F,
  threads = 1
)

Arguments

genomeFasta: path to file to process.
outIndex: path to output index.
overwrite: overwrite existing output files, TRUE or FALSE (default).
threads: number of threads to use, default is 1.

Value

Path to index

Author

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))