Hi. All good day. I was following the Atacama and moving pictures tutorial on my analysis using Qiime 2017.7.
I found some work around for the analysis that i need such as generating featuretable.biom (similar to Qiime1) with the taxonomy metadata using the qiime taxa collapse. I am thinking of exporting the generated featuretable.biom in Qiime1.9.1 to filter chloroplast, mitochondria and other unwanted sequences.
However, I cannot think of any work around to use the filter featuretable.biom generated in Qiime1 in order to be used in alpha and beta diversity in Qiime2 based on the moving picture tutorial ( I think it is really impossible.) For example,
qiime diversity core-metrics
--i-phylogeny rooted-tree.qza (i want to filter unwanted sequences in rep seq)
--i-table table.qza (i want to used the featuretable.biom filtered in Qiime1 in here)
--p-sampling-depth 1109
--output-dir core-metrics-results
If not, is there away that I can filter chloroplast, mitochondria and other unwanted sequences from the featuredata[sequences] and featuretable[frequency] prior generating tree for phylogenetic diversity analyses? I wanted the rooted-tree.qza and table.qza to be free of other sequences (chloroplast, mitochondria).
Please do let me know that what i what to do in here is correct. Thank you very much.