Discarded results produced by q2-cutadapt's trim-paired when working with mixed-orientation reads

[SoilRotifer (Mike Robeson)]

Hi @alison,

You can use this approach and see if it helps:

q2-cutadapt output

Good news @jessica.song! I think I solved this. First, thank you for sending me the PDF describing the protocol. I noticed a key statement: pairs of primers (Fw-Rev or Rev-Fw) had to be present in the sequence fragments That is, this particular sequencing facility must expect mixed orientation reads. Therefore you need to enter in both primers for each of the --p-front-* commands (in 5’ - 3’ orientation). Like so: qiime cutadapt trim-paired \ --i-demu…

-Mike