How to Evaluate the Number of Successfully Annotated Reads in My Sample

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1

Hi, I have a very simple question. After generating the taxonomic bar plot with this code:

qiime taxa barplot
--i-table table.qza
--i-taxonomy taxonomy.qza
--m-metadata-file metadata.txt
--o-visualization taxa-bar-plots.qzv

Is there a plugin available to summarize how many reads have been successfully annotated in the taxonomic profile?

Thanks in advance.

2

Hello @jjj33,

If I remember your posts, I think you found the DADA2 stats table that summarizes the result of making ASVs.

Now you are asking about a similar table that summarizes the result of classifying ASVs.

How do you define 'successful'? For your data, how do you tell if a taxonomy is correct?

3

Hi,

In other words, I want to know the percentage of unused reads after using a classifier.

Thank you, Colin!

4

Okay!

Classification takes place on the ASV sequences, so all reads that made it into ASVs are included in this step.

While all ASVs receive a classification, some classifications are more specific than others. Is this what you're asking about?

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5

Classification takes place on the ASV sequences

Oh, I made a mistake. In this case, I just need to check the DADA2 stats table to see how many reads were filtered out (which solves my question).

By the way, I'm still curious:

some classifications are more specific than others

If I want to see how many ASVs are classified at the species-level resolution, is there a plugin that can conveniently achieve this?

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6

You can get these counts by running taxa barplot and saving the CSV file for a given level.

(ASVs can be 'overclassified' just like OTUs, when an ambiguous taxa is given a name far more specific than it should be. More species level labels may not be better.)

7

Noted, thank you!

Btw, happy Thanksgiving!

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