creating a 12-rank SILVA taxonomy with RESCRIPt

Library Plugin Support
1

This is a fantastic tutorial, thanks!
I have a quick question. I want to use the silva reference with the 12-rank taxonomy, not the 7-rank like this tutorial references. I can't figure out where in the pipeline I need to make changes to address this, though. I feel like it's somewhere in the filtering, but I don't know what to add or remove to clarify this. Can you help me?

Thanks in advance!!

2

Hi @aeriel.belk,

We had recently updated our SILVA taxonomy parser to allow you to select the exact taxonomy ranks you'd like to use via the --p-ranks flag. You can select these ranks for either the parse-silva-taxonomy or get-silva-data actions:

ranks
ranks1230×346 112 KB

That is, you can use this flag like so:

qiime rescript get-silva-data \
    --p-rank-propagation \
    --p-include-species-labels \
    --p-ranks domain kingdom phylum class subclass order family genus \
    --output-dir ...

or

qiime rescript parse-silva-taxonomy \
    --p-rank-propagation \
    --p-include-species-labels \
    --p-ranks domain kingdom phylum class subclass order family genus \
    --output-dir ...

You can re-install RESCRIPt following the instructions here. Note you'll need to be running QIIME version 2020.8.

I hope to update parts of the tutorial soon.

-Let us know how it goes!
-Mike

2 Likes
3

Wow, thanks for getting back to me so quickly! That seems like a really easy fix, I'll try it right now :slight_smile:

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