Hello! This is a conceptual question, but I'd like to hear your opinons here.
I'm running a 16S analysis on some old plant samples, performed through Roche454 pyrosequencing 5 years ago.
I used the latest version (gg_13_8) of the Greengenes database to build my taxonomy reference file and then performed the taxonomic analysis, resulting in the following barplot:
The dark blue part of the bars is labelled as 'k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__;s__'
Sadly, I think the problem is due to a bad primer choice (27 and 533).
I don't think there is any way to obtain something useful from these results, because the contamination affects more than half of the samples making comparisons impossible, but I'm asking just out of curiosity.
By reading the QIIME2 tutorial, I noticed the feature-classifier extract-reads method makes it possible to perform a training on the basis of the primers sequences, and it has been proven to improve results. I doubt that, but do you think this would make the results even slightly better?