run_multiqc: Generate combined QC report for Salmon and FastQC

In GREP2: GEO RNA-Seq Experiments Processing Pipeline

Description

run_fastqc generates a single HTML report from the fastQC reports and salmon read mapping results using MultiQC.

Usage

run_multiqc(fastqc_dir, salmon_dir, destdir)

Arguments

fastqc_dir	directory where all the FastQC files are saved.
salmon_dir	directory of the salmon files.
destdir	directory where you want to save the combined QC report.

Value

HTML report.

References

Philip Ewels, Mans Magnusson, Sverker Lundin, and Max Kaller (2016): MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. https://doi.org/10.1093/bioinformatics/btw354

Examples

## Not run: 
run_multiqc(fastqc_dir=tempdir(),salmon_dir=tempdir(),
destdir=tempdir())

## End(Not run)

GREP2 documentation built on Sept. 3, 2019, 9:05 a.m.