# FastQC Tips & 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:

```bash
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

```bash
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](https://shortlongseq.hashnode.dev/how-to-download-multiple-fastafastq-files), 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 .fastq.gz file name]` inside, to process in bulk.

### Option 3. MultiQC

As you know, after using FastQC, 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 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](https://www.youtube.com/watch?v=BbScv9TcaMg&list=PLIA2-lqNuhvFGAsB92N0v7Qi5xCxCNsYM) to learn more about this tool. You can also go [here](https://multiqc.info/docs/) to read more about how to install, 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.