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:
- 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?
- 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.