Remove primers when importing demuxed per-sample fastq

[Gil_Sharon]

Hi All ,
Long time Qiime user, new to Qiime2. Looking great!
I am importing data that has already been demultiplexed, but still has the primer. Is there a way to remove primers (EMP protocol) when importing, or after importing, directly on the demuxed qza file?

Also, I could not find the documentation from qiime tools in the plugins. where can I find it?

Thanks!
Gil

[thermokarst]

Hi @Gil_Sharon! If you are using the EMP Protocol, my understanding is that your demuxed sequences should already have the primers removed (that is part of the protocol). If this isn't the case with your data, and the primers are still present, you can take a look at this forum post to see an option for trimming the sequences during denoising, if using q2-dada2. We are planning on supporting a general purpose trimming tool at some point in the future (no ETA yet), but this would happen after importing data, not as part of an import step, as you suggested above.

@Gil_Sharon

Also, I could not find the documentation from qiime tools in the plugins. where can I find it?

QIIME 2 is interface agnostic, and as a result, provides a few different interfaces for users (see qiime2.org for some nifty screenshots), and those interfaces are all able to define their own specialized functionality. The qiime tools ... indicates to me that you are using q2cli, which is our official command line interface. The subcommand tools is a built-in q2cli command (one of those "specialized functions" I mentioned above), and isn't a QIIME 2 plugin, which is why you didn't see it in the list of available plugins. Unfortunately we don't yet have detailed documentation online for our interfaces, but, you can learn more about q2cli but appending --help to just about any command incantation:

$ qiime tools --help
Usage: qiime tools [OPTIONS] COMMAND [ARGS]...

  Tools for working with QIIME 2 files.

Options:
  --help  Show this message and exit.

Commands:
  export   Export data from a QIIME 2 Artifact or Visualization.
  extract  Extract a QIIME 2 Artifact or Visualization archive.
  import   Import data into a new QIIME 2 Artifact.
  peek     Take a peek at a QIIME 2 Artifact or Visualization.
  view     View a QIIME 2 Visualization.

Thanks!

[Gil_Sharon]

Got it. Thanks, Matthew!