callBowtie2: Call the Bowtie Alignment Tool

Description Usage Arguments Details Value Author(s) References See Also

Description

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

Usage

1
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 Dec. 7, 2018, 8:01 a.m.