I'm putting together a pipeline (qiime2-2017.10) to process our V4 MiSeq data that was prepped using a non-oriented library. Here's what I've got so far: orient all reads in the same direction (using in-house script) and remove any primers found for the R1 file. orient all reads in the same direct…

I was able to isolate the issue to my trimming and orienting step. In the rare case of a primer being present in only on read direction (either R1 or R2), that read half will get oriented (and potentially reversed complimented) whereas its pair will not. I’ve since updated my orient script to handle…

DADA2 with non-oriented library

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ebolyen (Evan Bolyen) April 22, 2018, 3:45pm 14

Hey @schillebeeckx,

A shot in the dark, is it possible that your forward and reverse reads are the same for one (or more) of your samples? Your problem sounds similar to this thread: