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
Not only can you merge the fastq files but your life might be easier if you do. For merging them, a simple `cat` will suffice. I should note that you don't have to be delivered 300 some odd files, you can request that whomever is doing the sequencing just give you a two files (assuming paired-end) per sample/library (the `bcl2fastq` program that they use to process the bcl files produced by the sequencer can trivially do this).

If you don't want to wait until all of the files are merged, you can likely just use a named pipe as input to fastqc. Something like:

    mkfifo foo.fastq.gz
    cat sample_L1_R1_???.fastq.gz > foo.fastq.gz
    fastqc foo.fastq.gz

Given that fastqc is written in java, I can't guarantee that it'll properly handle block gzipped files like that (the java gzip library has been broken for years). You can always `zcat` instead. I should note that the only reason process substitution likely wouldn't work is that fastqc names the output files after the input file name.

For 2. it depends a bit on what you want. The sequencing facility actually has an idea about that already (it's produced by the machine). It's easy enough to just ask them (they can also give you a break down of how many reads per sample, their average quality (also per sample), etc.). For our internal pipeline, I have a pdf produced with that sort of information, since it's a bit quicker to look first at a single table like that than to trudge through all of the fastqc files. BTW, fastqc also produces an HTML file with the images included. When I QC flowcells before sending results to our local groups those are what I personally look at...it's quicker than dealing with the zip files.