bowtie2_samtools {Rbowtie2} | R Documentation

## Interface to bowtie2-2.4.4 align function

### Description

This function can be use to call the bowtie2 wrapper which wraps the `bowtie2-align-s` and the `bowtie2-align-l` binaries.

### Usage

    bowtie2_samtools(
      bt2Index,
      output,
      outputType = "sam",
      seq1 = NULL,
      seq2 = NULL,
      bamFile = NULL,
      ...,
      interleaved = FALSE,
      overwrite = FALSE
    )

### Arguments

`bt2Index` | `Character` scalar. The path where the bowtie2 index files are located. Include the basename of the index files at the end of the path (i.e. path_to_index_dir/index_basename). Do not include the bowtie2 index file extension (.bt2 or .bt2l)
`output` | `Character` scalar. The path where the alignment output file should be created. Include the basename of the alignment file at the end of the path (i.e. path_to_output_dir/output_basename). Do not include the alignment file extension (.sam or .bam).
`outputType` | `Character` scalar. Specify the output alignment file type. Default is set to "sam" but can also be changed to "bam".
`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`.
`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`.
`bamFile` | `Character` vector. A path to a bam file that contains unaligned reads. If a bam file is provided then seq1 and seq2 must be set to `NULL`
`...` | Additional arguments to be passed on to the bowtie2 wrapper. See below for details.
`interleaved` | `Logical`. Set `TRUE` when files are interleaved paired-end sequencing data.
`overwrite` | `Logical`. Force overwriting of existing files if setting `TRUE`.

### Details

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

### Value

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

### Author(s)

Zheng Wei

### References

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

### Examples

    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")

    ## Sam file created
    bowtie2_samtools(bt2Index = file.path(td,"lambda_virus"), output = file.path(td,"example"), seq1 = reads_1,
    seq2 = reads_2, overwrite = TRUE)

    ## Bam file created
    bowtie2_samtools(bt2Index = file.path(td,"lambda_virus"), output = file.path(td,"example"), outputType = "bam",
    seq1 = reads_1, seq2 = reads_2, overwrite = TRUE)

[Package Rbowtie2 version 2.0.0 Index]