taxonomy db problem

[shinseung]

Hello

I imported the database and ran vsearch.

Most of the taxonomy only comes up to "d__bacteria".

There is no "d__bacteria" in my database, starting at the phylum level.

Is there a separate format for the database import tsv file?

thank you.

[colinbrislawn (Colin J Brislawn)]

Helllo @shinseung,

Welcome back to the forums.

Can you post the full command you ran? I think that would help clarify what the vsearch plugin has done.

[shinseung]

Thank you for answer.

After editing the taxonomy file, some taxonomy names were correct.

The taxonomy txt file in the database has been imported into QIIME2, but there seems to be a problem with the format.

But still some come out as "d__Bacteria".

Is there a way to validate the taxonomy file?

There seems to be an invisible tab.

thank you.

[colinbrislawn (Colin J Brislawn)]

OK.

Can you post

• the command you ran to import the database
• the vsearch command you ran
• the first few lines of the database file before import

@shinseung

Is there a way to validate the taxonomy file?

It's a tab separated values file (TSV), but other than that I'm not sure we have a stand-alone validator. The RESCRIPt plugin does provide a lot of functionality. Check out this section of the tutorial about editing taxonomy.

[shinseung]

The database is customized.

My guess is that the taxonomy format of gtdb is the problem.

'-' or '#' goes into the feature id.

Of course, only "d_Bacteria" came out when vsearch was performed after importing and removing - and #.

The gtdb taxonomy file was created by extracting the header of the fasta file.

Attach the taxonomy file.

thank you.add.txt (4.8 MB)

[SoilRotifer (Mike Robeson)]

When we see cases in which most of the reads are poorly taxonomically assigned, it is likely that your sequences are not in the same orientation as the reference database. Here are a few threads that may help:

Lots of Unassigned reads

Welcome to the forum @victoriamesa! The 50% unassigned is a pretty clear indicator: your reads are probably in mixed orientations. The classify-sklearn method currently only supports classification of sequences that are in a single orientation. However, the classify-consensus-vsearch method can classify mixed orientation reads just fine. Could you give that method a try and let us know what you see? Thanks! But @sixvable is also correct: Even though this is probably not what is causing this…

Improving taxonomic classification

Hello everyone, My colleagues and I are doing the analysis of some low biomass samples with Qiime 2 (v2021.4). It's the first time that we do a microbiota analysis and we have found some strange results. In our Feature table we have a total of 56 samples, 4 commercial mock community replicas and some negative control samples. We have trained the classifier with the SILVA database following the instructions described in "Moving Pictures" and "Parkinson's Mouse" tutorials and then we have taxonom…

Host DNA or incorrect classifer workflow leading to high percentages just domain level classification

Hi @David_Bradshaw, I think much of what you have looks fine. Just a couple comments / suggestions: EDIT (05/22/2023): If you are running qiime rescript get-silva-data, there is no need to run the above command, as get-silva-data runs this for you behind the scenes. My mistake, this command should be run. I'd avoid removing Eukaryotes. A good classifier will contain a bunch of "outgroup" taxa. That is you should want to identify Eukaryotes, or any other "bad" items. Otherwise, Eukaryotic se…

@shinseung

There is no "d__bacteria" in my database, starting at the phylum level.

When it is not possible to achieve an exact or near-hit to any of the reference sequences, the classifier will return the Lowest Common Ancestor (LCA) taxonomy of similar sequences.

-Cheers!
-Mike