I am having a dilemma -- I am using an Illumina MiSeq to sequence MHC in songbirds (which can have many alleles per individual). I was able to create a primer to get sequences that range from 370-420 bp (due to indels and differences between subspecies). This means some sequences will not have substantial overlap if I use V2. In the past I have used V3, but my new genomics core seems to not want to use V3 due to its issues (which is still don't fully understand).
I am trying to determine what is more risky, having only 80 bp of overlap if I use V2 or having more overlap, but experiencing some issues (again which I don't understand) using V3.
Any advice is appreciated.