Hi @E.Kamil, if you used the V3-V4 primers and your amplicon size is around 460 bases then the issue is that 150bp paired-end sequencing will not have any overlap. For example, if the forward read starts at the 341bp position it will end around the 491bp position while the reverse read will begin at the 805bp position and end around the 655bp position. You can see that with this sequencing method there is a gap between the 491bp and 655bp positions and no overlap from your forward and reverse reads. Therefore, you will not be able to merge these reads. You may just have to use the forward reads and map only to the V3 region, but @ChrisKeefe or @thermokarst might have a better idea.
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