Dear all, based on my post https://forum.qiime2.org/t/strange-taxanomy-based-on-silva-database/20031?u=yuzhang I aim to use another database to assign my rep seq. First, I exported my rep seq from qiime2. Second I used the RDP web tool http://rdp.cme.msu.edu/classifier/classifier.jsp to assign th…

Hi @YuZhang , [image] YuZhang: based on my post https://forum.qiime2.org/t/strange-taxanomy-based-on-silva-database/20031?u=yuzhang I aim to use another database to assign my rep seq. The consensus in that post was to try using the SILVA 132 release. Why not do that? As noted in that post …

Thanks for your attention. First, I dont use the silva 132, because I looked up some articles and burkholderia-Caballeronia-Paraburkholderia still appeared when using 132 version，such as this article: Redirecting . Second, I indeed overlooked the second way you advised, because I browsed the forums…

[image] YuZhang: I looked up some articles and burkholderia-Caballeronia-Paraburkholderia still appeared when using 132 version Okay I am not sure what release that label first appeared in — it is just indicating that the genus is unresolvable/contested between those 3 genera, so they concate…

Thanks sir, I aim to try the NCBI-refseqs 16S first.

Hi，sir. When I perform the code below: qiime rescript get-ncbi-data \ --p-query '33175[BioProject] OR 33317[BioProject]' \ --o-sequences ncbi-refseqs-unfiltered.qza \ --o-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza It happens this error. [1627374440(1)] What's wrong?

please check the forum archive, this is due to incorrect installation/compatibility and has been answered elsewhere: [image] trouble with rescript Library Plugin Support Thank you very much for your help! Unfortunately, we have tried to use the 'orient-seqs' script but it…

Sir，thanks for your attention. I managed to use the NCBI database, but appeared a new problem. I want to retain Bacteria only. So I run the code below: qiime taxa barplot \ --i-table table-dada2-4.qza \ --i-taxonomy ncbi-taxonomy-4.qza \ --m-metadata-file metadata.txt \ --o-visualization ncbi-bar…

Use --p-exclude Archaea Eukaryota. However, I'd advise against removing these groups, as you'll want to keep off-target / outgroup taxa in your database. Otherwise you'll likely identify many taxa incorrectly as "d__Bacteria; ;", when in fact they may be Archaea or Eukaryota. See: [i…

Thanks,sir. I'm still a little confused. Even if I retain Archaea Eukaryota, I would still only focus on the bacteria in the downstream analysis, so I would still filter out the archaea in the downstream analysis (I used the phyloseq. How is this different from the current deletion

Hi Nicholas，an Another question, I found that NCBI database is much smaller than SILVA and RDP, so if I classified 16s to this database, and wrote an article, will the reviewer question it?

Import RDP classifier output taxonomy file into qiime2

Technical Support

Nicholas_Bokulich (Nicholas Bokulich) July 27, 2021, 9:25am 8

please check the forum archive, this is due to incorrect installation/compatibility and has been answered elsewhere: