FastQC command line usage

Question

[edus_bioinfo]

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.

[GenoMax]

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.

Answer 1

[nkabo]

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

fastqc --noextract --nogroup -o fastqc *.fastq.gz

[GenoMax]

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

[nkabo]

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