When running QIIME with SILVA DB, we get many results classified as D_0__Bacteria; D_1__Tenericutes; D_2__Mollicutes; D_3__Mollicutes RF9 … but in the SILVA DB webpage there is no such a group: may this be a mistake and RF9 mean RF39 really?
Thank you for your help. Regards. Paolo
Very interesting question. Could you please give more information on how you are performing your classification? E.g., classification method, whether you are training your own classifier, etc.
It looks like there is an “RF9” in the SILVA 132 release:
$ grep 'RF9' SILVA_132_QIIME_release/taxonomy/taxonomy_all/99/taxonomy_7_levels.txt AF001742.1.1469 D_0__Bacteria;D_1__Tenericutes;D_2__Mollicutes;D_3__Mollicutes RF39;D_4__unidentified rumen bacterium RF9;D_5__unidentified rumen bacterium RF9;D_6__unidentified rumen bacterium RF9
So if this is a misannotation you should take that up with SILVA (and please report back here! this is an error that could affect lots of QIIME 2 users).
thank you for your reply. We did the analysis a few months ago clustering reads into OTUs with 97% similarity through an open reference approach (pick_open_reference_otus.py script), using the UCLUST algorithm. For taxonomy the SILVA database release available at the time was nº 128. Do you think these Mollicutes have been re-classified in the meantime (in release 132)? I guess I’ll have to ask the SILVA people. Thank you. Paolo
Names changes are possible — check the SILVA releases from their website (not the browser, which is presumably the latest release).