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.
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.
After installing FastQC, you can simply run the code below:
fastqc --noextract --nogroup -o fastqc *.fastq.gz
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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You will need to download the resulting html files to view after you run the command below.