Diversity plug-in error

[Nicholas_Bokulich]

@LauraMason

Ok so just to recap, it would be best at this point to filter my reads for chimeras in Qiime1 (this was included in my original workflow), and then import them into Qiime2 for demultiplexing, OTU picking via vsearch etc? (You’re right, this is sounding suspicious).

No need to use qiime1 for chimera filtering. QIIME2 can do this for you after OTU picking — see this tutorial.

The earlier you get your data into QIIME2, the better (since qiime1 is no longer officially supported, it will be more difficult for us to diagnose problems originating there).

@LauraMason

As far as importing raw 454 data into Qiime2: My data are saved as .fna files. The Imports tutorial seems to cover this, but I wasn’t sure if it was the right step for my data the first time I tried it. The vsearch error I got was most likely operator, but I’ll post again if I run into problems.

If you only have .fna data, it looks like you will need to demultiplex in QIIME1 and import qiime1-demultiplexed data. This is covered in the vsearch tutorial.

So just to recap:

1. you have 454 data as .fna (no quality scores)
2. demultiplex in QIIME1
3. import to QIIME2 as SampleData[Sequences] as covered in the OTU picking tutorial
4. OTU pick with q2-vsearch, as described in the OTU picking tutorial
5. Chimera filter using q2-vsearch, as described in the chimera tutorial
6. QIIME on.

I hope that helps!