bowtie2: Interface to bowtie2 of bowtie2-2.2.3
In Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval

Description Usage Arguments Details Value Author(s) References Examples

View source: R/bowtie2.R

This function can be use to call wrapped bowtie2 binary.

1 2	bowtie2(bt2Index, samOutput, seq1, ..., seq2 = NULL, interleaved = FALSE, overwrite = FALSE)

`bt2Index`	`Character` scalar. bowtie2 index files prefix: 'dir/basename' (minus trailing '..bt2' of 'dir/basename..bt2').
`samOutput`	`Character` scalar. A path to a SAM file used for the alignment output.
`seq1`	`Character` vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in seq2. And it can also be interleaved file paths when argument interleaved=`TRUE`
`...`	Additional arguments to be passed on to the binaries. See below for details.
`seq2`	`Character` vector. It contains file paths with #2 mates paired with file paths in seq1. For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=`TRUE`), it must be `NULL`.
`interleaved`	`Logical`. Set `TRUE` when files are interleaved paired-end sequencing data.
`overwrite`	`Logical`. Force overwriting of existing files if setting `TRUE`.

All additional arguments in ... are interpreted as additional parameters to be passed on to bowtie2. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8 –no-mixed") with white space splited just like command line, or put them in different Character (e.g. "–threads","8","–no-mixed"). Note that some arguments("-x","–interleaved","-U","-1","-2","-S") to the bowtie2 are invalid if they are already handled as explicit function arguments. See the output of bowtie2_usage() for details about available parameters.

An invisible Integer of call status. The value is 0 when there is not any mistakes Otherwise the value is non-zero.

Zheng Wei

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.

td <- tempdir()
## Building a bowtie2 index
refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"),
full=TRUE)
bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads 4 --quiet",overwrite=TRUE)
## Alignments
reads_1 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads",
"reads_1.fastq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads",
"reads_2.fastq")
if(file.exists(file.path(td, "lambda_virus.1.bt2"))){
    cmdout<-bowtie2(bt2Index = file.path(td, "lambda_virus"),
       samOutput = file.path(td, "result.sam"),
       seq1=reads_1,seq2=reads_2,overwrite=TRUE,"--threads 3");cmdout
    head(readLines(file.path(td, "result.sam")))
}