FastQC and HISAT2

Question

[Jaber]

Hello everyone,

I'm encountering an issue where, whenever I try to run HISAT2 or FastQC in the terminal, they don't execute and instead prompt a window asking which software to open them with.

Although I can run FastQC by clicking on it directly, it doesn't work in the terminal.

I have the appropriate JRE installed.

Thank you in advance for your help!

[pinheirofabiano]

what's your OS? please tell us the command you are using to call FastQC.

[Jaber]

Many thanks, I use windows 11, the command is fastqc, it is already in the path, I checked it manually, and when I run this command in the terminal, it asks me to choose how I prefer to open this file.

thank you

Answer 1

[GenoMax]

I use windows 11, the command is fastqc, it is already in the path,

Does that mean you are using WSL2 i.e. linux on windows or are you using Windows directly?

fastqc is a wrapper perl script on windows/linux. You will need to have perl available for the program to work directly from the command line.

[Jaber]

Thank you, Yes I use linux on windows, I installed perl, the option to choose which software I want to open the file with have not disappeared, and it still don't work.

fastqc Data/demo.fastq -o Data/

and still didn't work

I am in the correct directory, I am wondering why it still don't work?

Any help is really appreciated?

I downlaoed the fastqc from this website: https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

is there another way to install it ?

[GenoMax]

You seem to have done the right steps (and I assume you are familiar with $PATH and concept of relative paths). Do you also have java installed? FastQC is a java application and requires a java runtime.

[Jaber]

Thank you, it worked almost after two months of struggle,

I nearly deleted everything and reinstalled it, I assume the problem was something that had to do with the cache and now it is working thank you a lot.