How to: multiQC ‐ summarize fastQC files - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki

What you want to do: create a summary of the fastqc results of a directory of fastq files.

Here's how:

1. Run fastQC to generate the data for each .fastq file in a directory

module load fastqc
fastqc *.fastq.gz

2. Run multiQC to summarize the big pile of fastQC results

module load multiqc
multiqc [directory name]  # use a "." for the current directory 

3. Download the multiqc output.