HowTo:FASTQC

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Installation

 $ conda install fastqc 

If you have a problem to run fastqc afterward, with "No fonts found", install the following packages.

 $ conda install font-ttf-dejavu-sans-mono fontconfig 

Run

 $ mkdir fastqc_out
 $ fastqc my_file.fastq -o fastqc_out 

If you want to make a single report for all fastq files,

 $ cat *.fq > merged.fq
 $ fastqc merged.fq -o fastqc_out 

If your files are compressed,

 $ zcat *fq.gz | fastqc stdin -o fastqc_out