To create a pre-trained classifier provided by QIIME2 using RESCRIPt

2

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2.2 years ago

yeshirata ▴ 20

Hello all,

I would like to use Rescript to create the following pre-trained classifier provided by QIIME2.

（pre-trained classifier）Silva 138 99% OTUs full-length sequences (MD5: b8609f23e9b17bd4a1321a8971303310)

I have created a classifier according to the Tutorial at the following site, but I am not sure how far I need to go to create exactly the same as the pre-trained classifier provided by Qiime2.

If anyone has any advice, I would appreciate it if you could open it.

Thank you in advance.

RESCRIPt rRNA 16S Qiime2 SILVA • 1.7k views

ADD COMMENT • link updated 2.2 years ago by andres.firrincieli 3.8k • written 2.2 years ago by yeshirata ▴ 20

3

Entering edit mode

To fix the problem you were describing in this post you should run the following chunk of code with the option --p-no-rank-propagation

qiime rescript parse-silva-taxonomy \
    --i-taxonomy-tree taxtree-silva-138.1-nr99.qza \
    --i-taxonomy-map taxmap-silva-138.1-ssu-nr99.qza \
    --i-taxonomy-ranks taxranks-silva-138.1-ssu-nr99.qza \
    --p-no-rank-propagation \
    --p-include-species-labels \
    --o-taxonomy silva-138.1-ssu-nr99-tax.qza

ADD REPLY • link 2.2 years ago by andres.firrincieli 3.8k

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