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How to deal with 16s V3V4 region length variation?

Dear all,

First of all sorry that this is not a 100% bioinformatics related question. I am analysing 16s V3V4 region metabarcoding data at the moment. I have some sequences that are shorter than 400 bp like round 300 bp or so. I guess those are the result of non-specific priming and should be removed, right? If so were is normaly the cut?

Thanks in advance.

sequencing next-gen metabarcoding

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