FastQC Tips & MultiQC

Photos via FastQC and MultiQC

There are several ways to process multiple FASTQ files through FastQC. I will demonstrate two ways you can execute and lastly, introduce MultiQC.

Option 1. Run Multiple Files in the fastqc Command

This option may be a bit crude and tedious, but if you are new to using Linux/Ubuntu this will help.

The command to execute FastQC in bulk is below. Replace the bracket with the correct file name:

fastqc [insert FASTQ file1 name] [insert FASTQ file2 name] [insert FASTQ file3 name]

The file you are trying to process is in .fastq.gz so make sure you are correctly inputting the file name. To show you an example:
fastqc SRR8238941_1.fastq.gz SRR8238941_2.fastq.gz SRR8238942_1.fastq.gz

Make sure you put space between each file, otherwise it will show an error message and have to redo this process again.

Once you are used to using Linux/Ubuntu. You can try using this command:

fastqc *.fastq.gz

What this command does is it will process all the files that are in .fastq.gz format. Pretty nifty, right? Now onward to the next one.

Option 2. Creating Script to Execute

In my article here, I showed you how you can create a script to process files in bulk for downloading FASTQ files from NCBI. Applying the same concept you will create a bash script using sh [insert script file name] command, with multiple lines of fastqc [insert file name.fastq.gz] inside, to process in bulk.

Option 3. MultiQC

As you know, it’s quite a grueling process to run and check each FASTQ file through FastQC especially when you have lots of data to process. MultiQC addressed that problem by analyzing and compiling many FASTQ files into a single report (HTML file).

You will need to transfer the HTML file back to your local PC to view the report.

You can go here to learn more about this tool. You can also go here to read more about how to configure and use this tool. If you are trying to install this on Linux/Ubuntu environment, go to the “Installation with pip” section in the document.

In the next article, I will be discussing the last part of the quality control process, trimming.