Make.contigs, maxee, non-overlaping reads


I am running since a long time now Mothur on my V4 sequenced samples. I like this program a lot especially the error correction feature of make.contigs. My primers do not perfectly align, like 50nt. Would it be a good thing to use maxee error check on those non-overlaping (or is it already being done?) small sequences to improve error discarding early in the process. Like if I run maxee=2 and deltaq=6, would it flag as N incorrect nulceotides in the csmall bits that do not overlap so the can be discarded?


Personally, for my V4, I first make my contigs using other software (mefit) that I think allows to a more complex handling of the problem of the lack of full overlapping… But still I discard 40% of the reads (all the non-overlapping for at least 50, plus those with bases Q<30 in any of both reads, or any ambiguity, or…).