Metadata base filtering & re-running alpha and beta diversity metrics

Hi,

I have a quick question. I have a metadata containing burnt and unburnt site and fire dates… I looked at all my data and performed alpha and beta diversity to compare burnt and unburnt sites, but I want to look at only the burnt sites, specifically the fire dates.

My question is, I have filtered my data to show only the burnt sites, but I am confused on the next steps.

  1. Since I am starting with a new table.qza, which I then turn to a .qzv file, do I have to do the phylogeny tree again prior to calculating alpha and beta diversity, and or will the command automatically know to only look at those samples which I have in the new, filtered table?

  2. To do alpha and beta diversity analysis, I determined a new sampling depth, based on the new table, is this correct?

  3. Is there a way for me to do a PCA instead of a PcOA, or should I just export the data and use it in R-studio?

I would recommend rebuilding your tree.

Yes!

This is not possible in QIIME 2 - you will need to export.

Keep us posted! :qiime2:

Last question,

I have been running the analysis with the Metadata I used for when I analyzed all of my samples. Am I supposed to trim this as well, or is this fine? When I automatically get a message listing all the unburn samples and saying they were not included in the analysis.

This should be fine.

I don’t understand this statement - can you please provide the text from the original message, copy-and-paste please.

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