bowtie2Par: Set or Query Bowtie2 Parameters

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

Set or Query Bowtie2 Parameters

Description

Set and retrieve named parameters that control the Bowtie2 alignment program.

Usage

bowtie2Par(...)
bowtie2Par( <name>=<value>)

bowtie2Par.defaults( optionsFile)

getBowtie2Version()

Arguments

...	parameters to query, or name-value pairs for setting parameters
optionsFile	name of a DuffyNGS_Options that contains Bowtie2 parameters to be set

Details

Bowtie2 uses several command line parameters that affect its runtime behaviour, and this utility provides a common interface to setting and retrieving those Bowtie2 parameters. To see all current parameters, use bowtie2Par().

Required parameters at present:

Program is the full pathname to the Bowtie2 executable program

IndexPath is the pathname to the folder of all needed Bowtie2 index files

GenomicIndex is the basename of the Bowtie2 Index to be used for the genomic alignment phase of the pipeline

Calling bowtie2Par.defaults() with no optionsFile will use values from the environment variables: BOWTIE2_PROGRAM, BOWTIE2_INDEX_PATH, and BOWTIE2_INDEX_FILE, respectively.

Value

For bowtie2Par(parameter) the currently set value of that parameter, or an error if that parameter is not set.

For getBowtie2Version(), the current version of Bowtie2 as a character string

See Also

fastqToBAM for a higher level wrapper to calling Bowtie buildBowtie2CommandLine for the utility that constructs valid Bowtie2 command lines. callBowtie2 for invoking the Bowtie2 alignment program. buildBowtie2BuildCommandLine for the utility that constructs valid Bowtie2-build command lines. callBowtie2Build for invoking the Bowtie2-build index creation program.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.