Produce table with ASV, assignation, perc identity, number of reads per sample

[alexcussigh0]

Hi everyone!

I have applied a qiime2 pipeline for the metabarcoding on fresh water eDNA using the 12s MiFish primers.
I have managed to obtain a TSV using qiime metadata tabulate on my classified consensus blast/VSEARCH denoised sequences.

I was wondering if there is a chance to obtain a complete TSV table with for each ASV obtained:
taxonomic assignation, percentage of identity, sequence, number of reads assigned all separated for each samples.

I hope I made myself clear,
thank you so much for the attention

[Mehrbod_Estaki]

Hi @alexcussigh0,
I think the information you are looking for (mostly) already exists through various artifacts which you probably already created. I'm not sure if there is an easy way to combine all of them within Q2, (there may be, I'm just not thinking hard enough about it atm) but probably the easiest way is to export the various tables into your preferred data wrangling program and combine them there. Below I've outlined where all of your requested data are. In almost all of the various visualization artifacts below there wil be a "download" button that will let you download the needed tables.

I'm going to refer to the Moving Pictures tutorial artifact names here for demo:

Sequence:
The rep-seqs.qzv artifact will show the hashed Feature/ASV ID and its corresponding sequence:

Taxonomy:
The taxonomic assignment of those features are in the taxonomy.qzv artifact:

# of reads assigned:
Look in the Feature Detail tab in the table.qzv

number of reads assigned all separated for each samples:
If I understand this correctly, this is basically just your table.qza. You can export this out of QIIME 2 in a tsv format like so:

qiime tools export table.qza --output-dir exported
biom convert -i exported/feature-table.biom -o feature-table.tsv --to-tsv

The second command there uses biom which is not a QIIME 2 program but does come preloaded in your Q2 environment.

percentage of identity
I'm not sure I understand what exactly you are referring to here. % identify of what?

Hope this helps

[alexcussigh0]

Thank you so much!
I was wondering if there is a way to produce a table with the sequence of the assigned ASV I have produced directly without merging the the rep-seqs.qzv artifact and the taxonomy.qzv artifact.

With percentage of identity I was referring to the Confidence value in the taxonomic assignment

[Mehrbod_Estaki]

Hi @alexcussigh0,

Sorry I'm not sure I fully understand what you are looking for exactly, I thought what you are describing already exists in the rep-seq.qza file. Can you show an example of you what you are looking for exactly?

Also just to clarify, in any of the artifacts above, you can visualize them alone directly using the metadata tabulate action. And as long as they share the same index (i.e. Feature ID) you can be merged multiple similar tables as well, ex:

qiime metadata tabulate \
  --m-input-file taxonomy.qza \
  --m-input-file rep-seqs.qza \
  --o-visualization taxo-table.qzv

However, if you are trying to include in there a table where the index is sample-id, and not Feature ID, you'll want to transpose that table first using qiime feature-table transpose