Error in openning FastQC

Question

[huynhthienphai]

Hi everyone,

I’m a beginner in Bioinformatics. I've recently used Debian 12 (VirtualBox 7.01) to practice some tools for RNA-seq analysis. I have some problems when running FastqC and IGV on the operating system. I downloaded FastQC windows/linux zip file. The scripts executed to install and run it to summarised below

$wget  https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
$unzip fastqc_v0.12.1.zip
$ cd FastQC
$chmod +x fastqc
$./fastqc

and then appears a black window with only the QC icon. And, running IGV is been faced with the same problem.

[GenoMax]

You need to setup X11 (X-Windows) for the graphical output to work on both ends. Some additional configuration may be required. I assume you are expecting to see GUI interface for FastQC. You can run FastQC without the GUI as shown by @bk11.

[Istvan Albert]

when you run via the VirtualBox you need to set it up so that you can view graphical UIs.

but for fastqc you would not need a GUI and you can just use bk11 's example

then for IGV you need to run the windows version of IGV and all you need is to mount the files to be visible from windows, so you would not need to run the GUI based program in Linux

Answer 1

[bk11]

Please see how the following command shows for you.

./fastqc -help

If is shows instruction for you, you can run like this-

fastqc -o output.html input.fastq

[friszd]

i don't know why, but this command doesn't work: 'Specified output directory 'output.html' does not exist' - i have just started using linux, so i'm absolutely don't know what to do

[GenoMax]

Post exact command you are typing.

[friszd]

fastqc -o output.html input.fastq 
ctrl+c ctrl+v

[GenoMax]

What is ctrl+c ctrl+v? You may actually be killing the running fastqc process.

If you run fastqc interactively (like what was shown above) then you need to wait until

fastqc -o output input.fastq

completes running. It can take some time.

Only provide output directory name. FastQC will automatically produce two output files per sequence file. One html report and other .zip archive.

[friszd]

after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run fastqc -o output input.fastq, terminal returns: " Skipping 'input.fastq' which didn't exist, or couldn't be read "

[GenoMax]

At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to command line. http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1.