UnzipAndMerge: Unzip and merge fastq files

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

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

See Also

atacRenamer atacQCReport

Examples

ignoreCheck() # warnning: run this for fast test only

td<-tempdir()
setTmpDir(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,"reads_1.fq")
reads_merged_2 <- file.path(td,"reads_2.fq")
atacproc <- atacUnzipAndMerge(fastqInput1 = reads_1,fastqInput2 = reads_2)
dir(td)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.