Bowtie2Mapping: Use bowtie2 aligner to map reads to reference genome

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

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")))
}

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.