get_bowtie2_cmd: Wrapper to build up the Bowtie2 command

Description Usage Arguments Details Value Author(s)

View source: R/get_bowtie2_cmd.R

Description

Wrapper function to build up the Bowtie2 command for the the system() call

Usage

1
2
get_bowtie2_cmd(inFile, samOutFile, referenceDir, method, p = 32,
  all = FALSE)

Arguments

inFile

File path to the in file(s)

samOutFile

Path to the sam output file

referenceDir

Path to the reference dir

method

Should ene-to-end or lcal mapping be used?

p

Number of used cores

all

Shoul the reads mapped to all possible positions on the reference [default = FALSE]

Details

This function is running internally in the map_dna_ref.

Value

character

Author(s)

Jochen Kruppa


jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.