buildBowtie2BuildCommandLine: Build a Bowtie2-build Command Line

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Build a Bowtie2-build Command Line

Description

Construct a Bowtie2-build command line that can create a Bowtie2 index file.

Usage

buildBowtie2BuildCommandLine(inputFastaFile, outputIndexFile, 
	optionsFile = "Options.txt", verbose = TRUE, debug = FALSE)

Arguments

inputFastaFile	a character string that contains comma separated full pathnames to existing FASTA files
outputIndexFile	base name for the set of index files to be created
optionsFile	the options file. This invokes bowtie2Par.defaults to set the location of the Bowtie2-build executable.

Value

a character string, suitable for passing to callBowtie2Build or to system.

Note

This blindly assumes that the 'bowtie2-build' executable is in the same folder as 'bowtie2'.

robertdouglasmorrison/DuffyNGS documentation built on April 13, 2025, 8:48 p.m.