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.
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huynhthienphai •
1 answer
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.
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.
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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.
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