FastQC command line usage
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5 months ago
edus_bioinfo ▴ 20

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 • 1.4k views
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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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5 months ago
nkabo ▴ 60

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

fastqc --noextract --nogroup -o fastqc *.fastq.gz
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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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Thank you for the comment. I usually use the code above, since I mostly work on short reads.

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