Hi all and sorry if my question has already been resolved. I am going to do all the bio info processing of my WGS for the first time so I obviously have some doubts, especially since it is sometimes difficult to know if what we did worked correctly or not. for each individual I have 8 fastq files. it's paired end so there are 4 R1 and 4 R2 files. I would like to know when and how should I merge them? if i merge the fastq i can do a cat file 1 2 3 4> newfile ? but if I merge the fastq to make a single R1 file and a single R2 file per individual is that information from which read is the mate of the other will be kept? because I would need this information for analyzes of structural variants.
Thanks in advance.