identify_adapters: identify adapters for paired-end reads

Description Usage Arguments Details Value Author(s) References Examples

View source: R/adapterremoval.R

Description

This function can be use to call wrapped AdapterRemoval binary for adapters identifying.

Usage

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identify_adapters(file1, file2, ..., basename = NULL, overwrite = FALSE)

Arguments

file1

Character vector. It can be file paths with #1 mates paired with file paths in file2 And it can also be interleaved file paths when argument interleaved=TRUE

file2

Character vector. It contains file paths with #2 mates paired with file paths in file1. For interleaved paired-end sequencing files(argument interleaved=TRUE),it must to be setted to NULL.

...

Additional arguments to be passed on to the binaries. See below for details.

basename

Character. The outputfile path prefix. Default: your_output

overwrite

Logical. Force overwriting of existing files if setting TRUE.

Details

All additional arguments in ... are interpreted as additional parameters to be passed on to identify_adapters. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8") with white space splited just like command line, or put them in different Character(e.g. "–threads","8"). Note that some arguments("–identify-adapters", "–file1","–file2","–basename") to the identify_adapters are invalid if they are already handled as explicit function arguments. See the output of adapterremoval_usage() for details about available parameters.

Value

An invisible Character vector of adapters for each mate.

Author(s)

Zheng Wei

References

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.

Examples

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td <- tempdir()
reads_1 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_1.fq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_2.fq")
adapters <- identify_adapters(file1=reads_1,file2=reads_2,
basename = file.path(td,"reads")
,"--threads 2",overwrite=TRUE)
adapters

Rbowtie2 documentation built on Nov. 8, 2020, 5:35 p.m.