Bowtie2Mapping: Use bowtie2 aligner to map reads to reference genome
In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

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

Use bowtie2 aligner to map reads to reference genome

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",
  ...
)

`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.

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.

An invisible ATACProc-class object scalar for downstream analysis.

Zheng Wei

atacRemoveAdapter removeAdapter bowtie2 bowtie2_build bowtie2_usage atacSam2Bam atacSamToBed atacLibComplexQC

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")))
}