A question about preparing file for lefse

Question

[hua.peng1314]

Hi all.I used RDP database to classify my 16S sequence.It has some categories like this: Lineage=Root;rootrank;Bacteria;domain;"Acidobacteria";phylum;Acidobacteria_Gp10;class;Gp10;genus I don't think "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|||g__Gp10" or "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|o__|f__|g__Gp10" are good choices. I am not sure whether "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|g__Gp10" is ok or I should change it to "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|o__Acidobacteria_Gp10_Unclassified|f__Unclassified|g__Gp10".Any suggeition. Thanks.

[5heikki]

Good choices for what?

Answer 1

[hua.peng1314]

Doctor Francesco Asnicar from has already sent my email.I will show it below.

the problem with the Gp10 genus is that it is a candidate genus and species. According to the NCBI the genera Gp10 has been renamed to Thermotomaculum. To be used with LEfSe, I would use the following taxonomy: k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|o__unclassified_Acidobacteria|f__Acidobacteria_subdivision_10|g__Thermotomaculum

Alternatively, if you want to use the genera provided by RDP, you can use the following taxonomy: k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|o__unclassified_Acidobacteria|f__Acidobacteria_subdivision_10|g__Gp10

Thanks doctor Francesco Asnicar for his patient kind responsibility and preciseness.

For my data have many categories like this and I won't check them all with NCBI but just the significant marks(Forgive my laziness).I will use "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|o__Unclassified_Acidobacteria_Gp10|f__Unclassified_Acidobacteria_Gp10|g__Gp10".

Thanks Francesco again.