Q2-cutadapt: how to handle untrimmed data?

Thank you very much for posting this tutorial. I am attemping to demultiplex data using the Ion Torrent 16S Metagenomics Kit that uses 12 primers to amplify 6 amplicons. Cutadapt is a great option b/c after I demultiplex I am hoping to trim with each primer separately and then bin each amplicon separately for downstream analysis. However, I am having problems implementing the “–trimmed-only” or “–discard-untrimmed” functions. Any help you can provide would be appreciated. Thanks!

Would you please post what your command is exactly? Then, if we don’t spot what is wrong right away, at least we can test it ourselves.

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Hi @David_Hilbert!

As @molecules mentioned, it would be pretty helpful for us to have some additional information in order to help you:

  • What version of QIIME 2 are you using?
  • What is the exact command or commands you are running? Copy and paste please.
  • If you are experiencing an error, what is that error? Copy and paste, if possible.

Thanks! :t_rex:

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