how to import these reads: Mixed-oriented or not?

[SoilRotifer (Mike Robeson)]

Hi @Wieneke, I think you can go ahead and import them as you normally would and then follow these two posts from the same thread.

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…

q2-cutadapt output

@jessica.song, I forgot to mention, that you’ll still need to orient this output into the same direction prior to any other downstream analyses. You can do this via the RESCRIPt action orient-seqs. -Good luck!

Let us know if this works.