Hi, I have a very simple question. After generating the taxonomic bar plot with this code:
qiime taxa barplot
Is there a plugin available to summarize how many reads have been successfully annotated in the taxonomic profile?
Thanks in advance.
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?
In other words, I want to know the percentage of unused reads after using a classifier.
Thank you, Colin!
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?
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?
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.)