Hi Everyone,

I am working on Whole Genome Sequencing and analysis of Human genome from illumina HiSeq platform with about 30X coverage. Each sample (human genome) have about 250-300 fastq.gz files, whom I am dealing with 'fastqc' for quality check using following command :

    /usr/local/bin/fastqc -t 8 -f fastq -o OUT/ -casava *.gz -noextract

Although it is running fine and generating equal number of "fastqc.zip" files which I unzipped using unzip '*.zip'. So, here I have 2 questions:

1. Can I merge two or more fastq files and then run fastqc on those merged files? If yes, how should I merge those fastq files?
2. I have to manually check 250-300 fastqc folder to know the quality by opening .html page. Is there any way where I can have summary of overall quality of the fastq files in a flowcell?

Please let me know your comments. I'll be highly thankful to you.

Best,  
Ravi
We have a script that will run fastqc and generate a [summary report][1] with the images from all the fastq files it was run on. You may also find it useful to systematically parse the fastqc_data.txt files from each run and combine the results that way.

The script is here, but may not be the most useful and documented thing ever... Depends on imagemagick to generate thumbnails...

https://github.com/metalhelix/illuminati/blob/cluster/scripts/fastqc.pl

Also uses this script:

https://github.com/metalhelix/illuminati/blob/cluster/scripts/thumbs.sh

 [1]: http://research.stowers.org/mcm/fastqc/fastqc_plots.html