fastQC: fastQC

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run fastQC

Usage

fastqc(fq1, fq2, output.dir, run.cmd=TRUE)

Arguments

fq1	Path to read1 fastq files
fq2	Path to read2 fastq files
output.dir	Output directory
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

FastQC aims to provide a QC report that detects problems originating from either the sequencer or the starting library material.

Value

Quality check report for sequence data. (e.g., .html)

References

FastQC: a quality control tool for high throughput sequence data. Andrews S. (2010).

See Also

http://www.bioinformatics.babraham.ac.uk/projects/fastqc

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.