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