I already looked at similar forum posts and FMT tutorial, but I really need somebody to clarify if I’m doing something good or totally wrong.
Due to financial reasons I first sent my winter and spring samples (including water and sediment) for sequencing, then summer and autumns samples (also water and sediment combined) - so this is 2 seperate runs. I analyzed 1st and 2nd run seperately.
Then I saw the option of merging on FTM tutorial:
qiime feature-table merge
qiime feature-table merge-seqs
It was a chance to merge whole year of sampling. So what did was: I copied my table.qza files and also rep-seqs.qza from 1. and 2. qiime2 analysis in new folder. I performed the above mentioned command. I also merged my 2 metadata tables and checked it with Keemei add-on.
At the moment I’m running qiime feature-classifier with silva database on this new (merged) rep-seqs.gza. Essencially, after I get my taxonomy_16S.qza & taxa_barplot.qzv, I’m going through Moving pictures tutorial (diversity analysis) but with merged data. Is that correect way to analyse merged Miseq runs?
Also, I saw option Group samples or features by a metadata category. I see that input file is FeatureTable[Frequency]. Just to be absolutely clear, is that my merged “table.qza”? Because I could group seperately samples of water in 1 year and sediment in 1 year and go throough same procedure (for diversity analysis and taxonomy).
Sorry for the long post and thanks for any information and advice regarding my doubts…