Nicholas Bokulich

That's correct --- those studies not mentioned in the Nature methods paper are described in the peerJ preprint. Studies 1683, 1684, 1689, and 1690 are NOT mock communities. They are...

Yes, Turnbaugh 1 = your 2011 PNAS paper. On Mon, Feb 15, 2016 at 4:41 AM, Greg Caporaso [email protected] wrote: > @nbokulich https://github.com/nbokulich, aren't the Turnbaugh 1 > sequences the...

> Thinking this discussion might be getting into a deeper problem, that calls for the necessity of being able to create a number of plots programatically (In my naive perspective)...

howdy! yes that's correct — [extract reads will orient the sequences](https://github.com/qiime2/q2-feature-classifier/blob/master/q2_feature_classifier/_cutter.py#L117-L119) (as long as the primers hit the F/RC sequences). would you like to modify this warning to clarify? Personally...

I agree, orienting in the same direction might need a little bit of testing to establish a working protocol, but one could use fairly loose %id and coverage settings to...

yeah that sounds reasonable... I think that %id is approx what deblur uses for pre-filtering reads, so maybe we can use that as precedent.

@mortonjt @fedarko FYI, @thermokarst and I have been talking about adding a vega scatterplots visualizer to q2-metadata, and it is on our radar for 2019. This visualizer would generate interactive...

> Maybe --i-explanatory vs --i-response or something like that?? +1

I agree, definitely worth updating! The effect on weights would probably be minor, but the newer primers are presumably what most new studies would be using, so important to update.

what about only performing train/test split on the metadata? And then you subsample the biom tables accordingly. This is what is done in q2-sample-classifier, and could be applied here.