18s data to analysis protist

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Hi @YuZhang,

If you are only interested in protists, you can filter your data by taxonomy.

PCR & Sequencing primers are always a bit "leaky" and often will hit off-targets. In this case I would not be surprised if you hit many non-protist eukaryotes.

A couple of tips:

  • Update to the newly QIIME 2 formatted SILVA 138 reference databases available here. Or you can make your own SILVA db using RESCRIPt. I recommend these as these will have a GreenGenes-like taxonomy annotation, none of that D_2__, ... mess. :slight_smile:

  • Also, there is a protist specific reference database you can try, PR2, and the PR2 primer database. I've not made use of this myself, but figured it might be of interest to you.

:microbe:

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