using older Silva or just latest in long timespan microbiome experiments

[colinbrislawn (Colin J Brislawn)]

Hello @fenny,

Welcome to the forums! :qiime2:

I don't have all the answers, but hopefully I can help assemble this data set. Let's dive in!

@fenny

We are following communities in wwt plants over a long periode where we sample regularly.

I'm glad you and your team were able to continue sampling over this last year.

@fenny

Unfortunately the raw data for early runs are no longer available (long story) but I do have the dada2 output. We only have raw data from june 2020 and later.

That is unfortunate, but still workable. Because DADA2 produces stable ASVs, if you proces future runs using the same version of DADA (same qiime2 version, q2-dada2 version, etc) then you can merge the feature tables and merge ASV sequences to get a unified output.

In fact, it's best to run DADA2 separately on each sequencing run, so you are off to a good start!

@fenny

I'm currently running 2021.11 with the 138 release of the silva classifier. The last previous experiments were analyzed with 2020.2 and silva 132.

While the version of Qiime2 should not make a huge difference, reviewer three is going to ask why the database changed.

I think you have outlined your options well. Here is what I would do:

@fenny

rerun the whole dataset in 2021.11 and silva 138 or whatever comes in the future

I like this option because it lets you incorporate all your data into a unified output, even the DADA2 results from that first run. When you merge and process at the very end, you get to use the newest databases and pre-trained taxonomic classifiers, along with any new features!
:qiime2:

(Of course, you could also process and merge the data you have now to demo this pipeline and see how the project is going! )