Taxonomy file creation query

[Nicholas_Bokulich]

Hi @Asha1,

@Asha1

Is there any method or coding to create taxonomy file for 21,789 sequence rather than manually?

Yes, there is a new QIIME 2 plugin that will do this for you. We have a tutorial for it on this forum:

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt - #7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Ben…

@Asha1

is it mandatory to give all level of taxonomy ( Kingdom to species) or geneus and species name is enough for running in qiime?

Nothing is mandatory but only genus and species is probably not enough for good classifications.

@Asha1

we have sequenced only v3-v4 region for our bacterial sample. Now, I have download whole 16srRNA sequence, is it mandatory to pick only v3-v4 target region alone from the sequence or could I use entire 16srRNA sequence for analysis in qiime? Using the entire 16srRNA sequence affect the analysis or not?

see the classifier training tutorial at docs.qiime2.org for more discussion of this. Short answer is you do not need to trim to the target region, but it is usually beneficial. And why not trim? It is a single command in q2-feature-classifier and a little more time to wait