trimming read files containing a mixture of forward and reverse primers

[SoilRotifer (Mike Robeson)]

Hi @adamsorbie,

I think this is what you're looking for:

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…

and this bit:

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!

-Mike