fastqc not recognized as comand in Windows

[kaleighbee30]

Hello! I'm trying to run FastQC on a group of ~1000 fastq files. I am able to get the GUI to work, but whenever I try to run the command from the Windows command line, I get the error: 'fastqc' is not recognized as an internal or external command, operable program or batch file.

Context if needed: My java version is 22.0.2. The GUI works just fine, but I'd prefer to automate. Other commands in the FastQC folder work as well, like typing in LICENSE.txt will pull up the correct txt file.

[s-andrews]

Sorry, I was on holiday when this came through.

Automation of large numbers of files on windows is not really staight forward. The launch script used for linux / mac is written in perl which isn't generally available on windows by default, and I'm not sure if I've ever tested to see if it would work if you add it.

The simplest option would be to run fastqc in a linux environment if you have one. If you dont and you're up for a bit of a test then you could try the following:

1. Install Perl on your windows machine https://www.activestate.com/products/perl/
2. Open a command (cmd) shell on your windows machine
3. Run fastqc as follows:

perl c:/Programs/FastQC/fastqc d:/data/*fastq.gz

Where you'd have to replace the locations of the fastqc program and the location of your fastqc files. If you're lucky then that will do an automated analysis of the files for you. You could even add --threads 8 (or whatever number of CPUs you have) to run the analysis in parallel.

Hope this helps