differences between qiime classifier and NCBI blast report for moving pictures tutorial

[gjahanmir (gh)]

Dear all,

In the Taxonomic analysis section of the moving picture tutorial, I attempted to address a question by comparing the results of the Blast analysis (as seen in the blast report from the visualization of rep-seqs.qzv) with the taxonomy classifier (taxonomy.qzv). I checked a few feature IDs and found discrepancies between the Blast results and the taxonomy classifier. The hits were classified as Eukaryota rather than Bacteria. Also in many cases, I saw "Uncultured bacterium clone" as hits.

I also found some that both method shows exact the same taxanomy while some only share same kigndom (Bacteria).

I would greatly appreciate it if anyone has encountered a similar situation before or if there might be a mistake in my approach.

2. Another question is related to the variability in the Taxonomy file for each feature ID, wherein different taxa are assigned. While some feature IDs provide detailed taxonomic information up to the level of genes and species, others only provide information up to the level of class.
   I am running Qiime on goolgle colab. Command "!qiime --version" shows : q2cli version 2023.7.0.

Thanks in advance,

[cherman2 (Chloe Herman)]

Hi @gjahanmir,

@gjahanmir

I checked a few feature IDs and found discrepancies between the Blast results and the taxonomy classifier.

I believe that his really boils down to the differences in the databases that you are using. Since they are not using the same database to classify features, they can have discrepancies as you are noting. I don't believe that this is a mistake in your approach.

@gjahanmir

nother question is related to the variability in the Taxonomy file for each feature ID, wherein different taxa are assigned. While some feature IDs provide detailed taxonomic information up to the level of genes and species, others only provide information up to the level of class.

This is a great question! The classifier only annotates to the taxonomic level that it is confident in. Sometimes that will mean that you get annotations down to the species sometimes you will only get annotations down to the class.

Another thing to note:
An annotation like this:

k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae

means that there was only confidence down to the family level.

While an annotation like this:

k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__; s__

means that there is confidence for an annotation down to the species but the database didnt contain genus and species information for the sequence.

I hope that helps!