Newbie here: I have recently done some chip-seq, and for each sample, I have different FASTQ files for forward and reverse reads (forward and reverse reads differentiated by -1 and -2 file extensions, respectively). There are a total of 12 samples. My question is: how do I deal with this. Do I want to combine the -1 and -2 (forward and reverse reads) for each sample, or keep them separate. Also, each of the 12 samples were run on 4 lanes, so I actually have 4 forward and 4 reverse reads for each sample. These I WILL combine before alignment.
Any suggestions would be welcome