This is probably a dummy question, but I haven't found an explanation and I want to be sure. When paired-end sequencing is done, there are usually 2 fastq files generated, one with "left" mates and the other with "right" mates.
Assuming that mates in the first file are read from the forward strand, are then mates in the second file read from the reverse strand?
If so, what is exactly written in the second file? A reverse complement of the read sequence (the corresponding sequence on the forward strand) or the pure reverse-strand sequence? And in which direction?