Bowtie2Mapping {esATAC} | R Documentation

## Use bowtie2 aligner to map reads to reference genome

### Description

Use bowtie2 aligner to map reads to reference genome

### Usage

    atacBowtie2Mapping(
      atacProc,
      samOutput = NULL,
      reportOutput = NULL,
      bt2Idx = NULL,
      fastqInput1 = NULL,
      fastqInput2 = NULL,
      interleave = FALSE,
      threads = getThreads(),
      paramList = "--no-discordant --no-unal --no-mixed -X 2000",
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacBowtie2Mapping(
      atacProc,
      samOutput = NULL,
      reportOutput = NULL,
      bt2Idx = NULL,
      fastqInput1 = NULL,
      fastqInput2 = NULL,
      interleave = FALSE,
      threads = getThreads(),
      paramList = "--no-discordant --no-unal --no-mixed -X 2000",
      ...
    )

    bowtie2Mapping(
      fastqInput1,
      fastqInput2 = NULL,
      samOutput = NULL,
      reportOutput = NULL,
      bt2Idx = NULL,
      interleave = FALSE,
      threads = getThreads(),
      paramList = "--no-discordant --no-unal --no-mixed -X 2000",
      ...
    )

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacRemoveAdapter` `removeAdapter`
`samOutput` | `Character` scalar. A path to a SAM file used for the alignment output.
`reportOutput` | `Character` scalar. The prefix of report files path.
`bt2Idx` | `Character` scalar. bowtie2 index files prefix: 'dir/basename' (minus trailing '.*.bt2' of 'dir/basename.*.bt2').
`fastqInput1` | `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 fastqInput2. And it can also be interleaved file paths when argument interleaved=`TRUE`
`fastqInput2` | `Character` vector. It contains file paths with #2 mates paired with file paths in fastqInput1. For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=`TRUE`), it must be `NULL`.
`interleave` | `Logical`. Set `TRUE` when files are interleaved paired-end sequencing data.
`threads` | `Integer` scalar. The threads will be created in this process. default: getThreads()
`paramList` | Additional arguments to be passed on to the binaries. See below for details.
`...` | Additional arguments, currently unused.

### Details

The parameter related to input and output file path will be automatically obtained from `ATACProc-class` object(`atacProc`) or generated based on known parameters if their values are default(e.g. `NULL`). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use `bowtie2Mapping` instead. additional parameters to be passed on to bowtie2. 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 as `Character` vector (e.g. c("–threads","8","–no-mixed")). Note that some arguments("-x","–interleaved","-U","-1","-2","-S","threads") 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.

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Zheng Wei

### See Also

`atacRemoveAdapter` `removeAdapter` `bowtie2` `bowtie2_build` `bowtie2_usage` `atacSam2Bam` `atacSamToBed` `atacLibComplexQC`

### Examples

    td <- tempdir()
    setTmpDir(td)

    ## Building a bowtie2 index
    library("Rbowtie2")
    refs <- dir(system.file(package="esATAC", "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="esATAC", "extdata", "bt2", "reads",
    "reads_1.fastq")
    reads_2 <- system.file(package="esATAC", "extdata", "bt2", "reads",
    "reads_2.fastq")
    if(file.exists(file.path(td, "lambda_virus.1.bt2"))){
        (bowtie2Mapping(bt2Idx = file.path(td, "lambda_virus"),
           samOutput = file.path(td, "result.sam"),
           fastqInput1=reads_1,fastqInput2=reads_2,threads=3))
        head(readLines(file.path(td, "result.sam")))
    }

[Package esATAC version 1.9.3 Index]