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FastQC command line usage

Hi,

I am supposed to run FastQC in linux server (I don't have chance to use graphical user interface) how can I use command line for running fastqc for my sequences? Thanks in advance.

command-line fastqc linux centos
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updated by LayneSadler LayneSadler • written by biology_inform • biology_inform

i dont have chance to use graphical user interface

You will need to download the resulting html files to view after you run the command below.

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written by GenoMax GenoMax

2 answers

After installing FastQC, you can simply run the code below:

fastqc --noextract --nogroup -o fastqc *.fastq.gz
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written by nkabo nkabo

Be careful about recommending --nogroup. If there are long reads (e.g. 300 cycles) then the plots become unwieldy to view.

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written by GenoMax GenoMax

Thank you for the comment. I usually use the code above, since I mostly work on short reads.

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written by nkabo nkabo

The FastQC installation process for Linux and Windows is just to download the zip file from their website. Then you can treat the unzipped FastQC/fastqc file as both a GUI and CLI program.

It needs Java as well: "README.txt: tested on Windows, MacOSX and Linux running the Oracle v1.6 to 1.8 JREs." JDK 19 worked fine for me

$ FastQC/fastqc -t 2 file_1.fq.gz file_2.fq.gz

  Started analysis of file_1.fq.gz
  Started analysis of file_2.fq.gz

  Approx 5% complete for file_1.fq.gz
  Approx 5% complete for file_2.fq.gz

Here -t creates 1 thread per file at 250MB of memory each

If you don't specify --outdir then it will create output reports in the same folder as the input files

For macOS Big Sur 11.7.2, I could not figure out how to run it from the command line and the UI file browser did not work either

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written by LayneSadler LayneSadler

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