Qiime demux summarize error with NextSeq data

Hi @ylor,

Do you have some reference sequences (and their associated taxonomy)? Also, what is your target amplicon here? There are some other options that don’t require training a classifier like:

  classify-consensus-blast    BLAST+ consensus taxonomy classifier
  classify-consensus-vsearch  VSEARCH consensus taxonomy classifier

Just to clarify, classify-consensus-blast is taxonomy assignment. As far as comparing OTU picking this tutorial is what you’ll want to look at.

Since the input is just a feature-table and some representative sequences, you actually have two ways you can do this:

  • You can either do dereplication (and chimera checking) directly on your SampleData[Sequences...] (similar to QIIME 1).

  • or you can perform OTU picking on your DADA2 ASVs.

The two aren’t mutually exclusive either, so you could try both as well.

Let me know if that helps!

Thanks @ebolyen.

I figured as much that those would be the possible routes for me to take. Having never generated my own reference sequences and taxonomy file, I am not sure what is all required in each of these files. Is there a specific format that the reference sequences need to be in? Can it just be a file containing fasta sequences downloaded from NCBI? How would I generate a corresponding taxonomy file? Can you provide me a little more guidance on how to generate properly generate these files so they are QIIME2 compatible?

Also, I am using several markers: 12s, 16s, coi and cytb. Would it be easier to generate a separate reference database per gene?

Thank you for bearing with me and answering all my questions!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.