I'm trying to run the deblur function for a paired-ends sequence, so for that I need to join the pairs before anything. But here's the issue, it seems like when I ran the code to join the pairs, it didn't really overlapped, it just added one in front of the other. Here's a screenshot from my interactive quality plot:
Hello!
Based on quality plots I would say that your reads are merged - one can see a strict line with no quality fluctuations - it is the overlap (join-pairs reset quality scores when region overlaps).
