Description Usage Arguments Value FastQC path Examples
Run the FastQC tool to generate HTML reports. FastQC may be installed from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
1 2 | run_fastqc(fastqc.files = NULL, dest.dir = "FASTQC", threads = NULL,
fastqc = "fastqc")
|
fastqc.files |
character vector of paths to fastq files. [DEFAULT = NULL]. |
dest.dir |
character string indicating directory to save results. [DEFAULT = "FASTQC"] |
threads |
an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1]. |
fastqc |
a character string specifying the path to the fastqc executable. [DEFAULT = "fastqc"]. |
character
string specifying the path of the output directory.
If the executable is in $PATH
, then the default value for paths
("fastqc"
) will work. If it is not in $PATH
, then the absolute
path should be given. If using Windows 10, it is assumed that FASTQC has
been installed in WSL, and the same rules apply.
1 2 3 4 5 | ## Not run:
fqFiles <- list.files(path = "fastqDir", pattern = "*.fastq", full.names = TRUE)
run_fastqc(fqFiles)
## End(Not run)
|
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