identify_adapters: identify adapters for paired-end reads
In Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval

Description Usage Arguments Details Value Author(s) References Examples

View source: R/adapterremoval.R

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

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

`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`.

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.

An invisible Character vector of adapters for each mate.

Zheng Wei

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

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