Hello, I followed your tutorial and analyzed my data. I am studying the bacteria associated with a forest tree and a beetle, using qiime2-2020.2.
By reviewing the taxa bar plot and the data structure (mitochondria,unnecessary samples…) I decided to clean my table.qza and rep-seqs.qza (commands below), in order to run a new analysis with filtered data, starting from the ‘tree generation for phylogenetic diversity analysis’ step.
Input: Feature table tableJ.qza and Representative sequences rep-seqsJ.qza
Filtering out unnecessary samples
qiime feature-table filter-samples
Filtering out all the organisms/organelles different from bacteria
qiime taxa filter-table
Filtering the sequences
qiime feature-table filter-seqs
One difference that I noticed is that my new Feature Table “tableJ_idfilter_138.qza“ is not interactive and I cannot directly assess the sampling depth (See screenshot).
My question is whether now I should set a low (e.g. 100) sampling depth in qiime diversity core-metrics-phylogenetic, since I want to use all the samples. During the first analysis, I set the sampling depth at 1164 and I am afraid that if I use this value now, some samples would be discarded.
Do you usually proceed in this way to analyze the alpha and beta diversity of only bacteria, without being biased by other organisms/organelles?