I want to look at original ChIA-PET datasets (FASTQ). It's a kind of paired-end sequencing. The same identifier has two paired sequences. Is there any tutorial on analyzing paired-end sequences? I'm a beginner on this. I don't know how to start this? Could anyone give me some suggestions?
A little more specific, I have two fastq files, 1.fastq and 2.fastq. each PET contains a tag and half linker. I suppose I need to remove half linker sequences first. I have an vague idea that the file also contains sequence quality. What tool can I use to get the quality for each PET? How do I calculate the quality for each PET?
Thanks a lot!