I have received paired-end reads from HiSeq Illumina platform. The PCR amplicon was 480 bp in length, 2*240.
In merging by DADA2, how will they have overlapping while they have no bases in common? I am just curious to learn what is the concept of overlapping in merging two reads(R and F) each other when they have been read 50:50.
For example, In my case PCR amplicon is 480 bp. It means 240 bp read from forward side and 240 bp from reverse side. It does not make sense to have a overlapping region there. This issue is not only for me, but also It think it is applied for everybody’s data; otherwise, there is a special explanation that I an unaware.
Please enlighten me!