adapter_content: Creates a sorted from most frequent to least frequent abundance table
of adapters that are found to be present in the reads at greater than 0.1% of the reads. If output_file is selected then will save the entire set of adapters and counts. Only available for macOS/Linux due to dependency on C++14.
Description
Creates a sorted from most frequent to least frequent abundance table of adapters that are found to be present in the reads at greater than 0.1% of the reads. If output_file is selected then will save the entire set of adapters and counts. Only available for macOS/Linux due to dependency on C++14.
Usage
adapter_content(infile, adapter_file = system.file("extdata", "adapters.txt", package = "qckitfastq"), output_file = NA)
Arguments
| Argument | Description |
|---|---|
infile |
the path to a gzipped FASTQ file |
adapter_file |
Path to adapters.txt file. Default from package. |
output_file |
File to save data frame to. Default NA. |
Value
Sorted table of adapters and counts.
Examples
r
if(.Platform$OS.type != "windows") {
infile <- system.file("extdata","test.fq.gz",
package = "qckitfastq")
adapter_content(infile)[1:5]
}