fastqc {fastqcr}

Run FastQC Tool

Description

Run FastQC Tool

Usage

fastqc(
  fq.dir = getwd(),
  qc.dir = NULL,
  threads = 4,
  fastqc.path = "~/bin/FastQC/fastqc"
)

Arguments

fq.dir

path to the directory containing fastq files. Default is the current working directory.

qc.dir

path to the FastQC result directory. If NULL, a directory named fastqc_results is created in the current working directory.

threads

the number of threads to be used. Default is 4.

fastqc.path

path to fastqc program

Value

Create a directory containing the reports

Examples

## Not run: 
# Run FastQC: generates a QC directory
fastqc(fq.dir)

## End(Not run)