SCUnzipAndMerge: Unzip and merge fastq files

SCUnzipAndMergeR Documentation

Unzip and merge fastq files

Description

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

Usage

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

scUnzipAndMerge(
  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

atacSCRenamer

Examples


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

td<-tempdir()
setTmpDir(td)


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