Benjamin Callahan comments

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                                            Benjamin Callahan

After Clustering ASVs of DADA2, what exactly to deal with the New OTU table?

You want to make sure that whatever you give `assignTaxonomy` (in this case `merged_seqtab`) can correctly get the DNA sequences in character format extracted from it by the `dada2::getSequences` function....

Different sequencing runs present different alpha diversity

Well, in downstream analyses of alpha-diversity, you will need to control for the batch effect, for example by including a batch term in any linear regression analyses of alpha-diversity.

Different sequence runs shows significantly different in alpha diversity

What alpha diversity metric are you analyzing here?

Different sequence runs shows significantly different in alpha diversity

Observed taxa is highly dependent on sequencing depth. Shannon Index is much less so, but not entirely immune to it. Could you recreate these plots from a set of samples...

Different sequence runs shows significantly different in alpha diversity

First, I would not use observed ASVs/OTUs as a metric. Looking at the Shannon results, I think it is reasonable that you should include run as a confounding factor in...

Hey

What is `any(duplicated(list.samples.names))`? That apparently has duplicate names in it. You can identify the duplicates with: ``` is.dup

Assign taxonomy loading time (ITS tutorial)

It shouldn't take that long. That said, I have not tested the latest UNITE db on an 8GB machine. A test that might be worthwhile is to try `assignTaxonomy` on...

Assign taxonomy loading time (ITS tutorial)

Sure... ``` sq10

Assign taxonomy loading time (ITS tutorial)

> The first 10 ASVs took about 7 min. Does that seem reasonable? That is longer than it should take, and suggests you are running into memory issues. Do you...

plot_frequency error

This looks like a bug, in that the zero-count samples are being removed as appropriate, but then either the row.names or some other variable is not being appropriately subset as...