callBowtie2: Call the Bowtie Alignment Tool

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

Call the Bowtie Alignment Tool

Description

Call Bowtie2 (or older Bowtie) to do an alignment of a file of FASTQ read data.

Usage

callBowtie2(bowtieCommandLine, wait = TRUE, verbose = FALSE)

Arguments

bowtieCommandLine	the Unix command line that will run Bowtie2. See buildBowtie2CommandLine
wait	should the calling function wait for Bowtie2 to finish
verbose	prints diagnostic and timing information

Details

Dispatches the call to Bowtie2 via the R 'system()' function.

Value

A list of diagnostic information:

timeIn	diagnostic timing information from proc.time before the call to Bowtie.
timeOut	diagnostic timing information from proc.time after completing the call to Bowtie.

Author(s)

bob Morrison

References

http://bowtie-bio.sourceforge.net/

See Also

buildBowtie2CommandLine for constructing the command. bowtie2Par for default settings. fastqToBAM for a higher level function for doing alignments.

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