I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.
In the "old" system you removed the opposite strand since that primer had a cleavable site to remove it.. Now how does it work with the paired reads? Do you still remove the opposite strand? if so: how do you "flip" the DNA to read from the opposite side? Or do they not cut one of the primers anymore and sequence 1 strand using 1 primer and the opposite strand with primer 2 ?