R: Unzip and merge fastq files

UnzipAndMerge {esATAC}

R Documentation

Unzip and merge fastq files

Description

Unzip and merge fastq files that are in format of bzip, gzip or fastq

Usage

atacUnzipAndMerge(fastqInput1, fastqInput2 = NULL, fastqOutput1 = NULL,
  fastqOutput2 = NULL, interleave = FALSE, ...)

unzipAndMerge(fastqInput1, fastqInput2 = NULL, fastqOutput1 = NULL,
  fastqOutput2 = NULL, interleave = FALSE, ...)

Arguments

`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`.
`fastqOutput1`	`Character`. The trimmed mate1 reads output file path for fastqInput2.
`fastqOutput2`	`Character`. The trimmed mate2 reads output file path for fastqInput2.
`interleave`	`Logical`. Set `TRUE` when files are interleaved paired-end sequencing data.
`...`	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

Examples


td<-tempdir()
options(atacConf=setConfigure("tmpdir",td))

# Identify adapters
prefix<-system.file(package="esATAC", "extdata", "uzmg")
(reads_1 <-file.path(prefix,"m1",dir(file.path(prefix,"m1"))))
(reads_2 <-file.path(prefix,"m2",dir(file.path(prefix,"m2"))))

reads_merged_1 <- file.path(td,"reads1.fastq")
reads_merged_2 <- file.path(td,"reads2.fastq")
atacproc <- atacUnzipAndMerge(fastqInput1 = reads_1,fastqInput2 = reads_2)
dir(td)

[Package esATAC version 1.2.3 Index]