silva138_V3v4/V4V5_human-stool_classifier.qza

Community Plugin Support
1

Hello:

Are there silva138_v3v4_human-stool_classifier.qza and silva138_v4V5_human-stool_classifier.qza or greengene version that I can download? I need these two to analyze stool samples.

Thanks,

Jin

2

Hi @jlli2000, welcome to :qiime2:!

We have an amazing plugin: RESCRIPt. You can use this make your own custom SILVA classifier as outlined here.

I'd also recommend the clawback plugin. The tutorial is available here.

-Cheers!
-Mike

-Mike

1 Like
3

Hi, Mike:

Thanks for your reply. I tried to use RESCRIPT to create human stool weight 16Sv3v4 classifier following the 16SV4 tutorial (extracted with 16SV3V4 primers). When I run this step:

qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads silva-138-ssu-nr99-seqs-V3V4-uniq.qza
--i-reference-taxonomy silva-138-ssu-nr99-tax-V3V4-derep-uniq.qza
--i-class-weight human-stool.qza
--o-classifier silva138-ssu-nr99-16SV3V4-human-stool-classifier.qza

I received this error message:

Plugin error from feature-classifier:

Number of priors must match number of classes.

Debug info has been saved to /var/folders/5y/kw01vx6n60g3zpwcgy2xnsqr0000gn/T/qiime2-q2cli-err-37pfr9ix.log

Do I need a specific human-stool.qza for 16SV3V4?

Thanks,

Jin

4

I assume you pulled human-stool.qza from readytowear?

As for the

This appears to be an unresolved issue as outlined in this thread. I would suggest either using the human-stool.qza full-length class weights or use your newly extracted V3V4 region w/o the class weights. Perhaps @BenKaehler might have some other advice here?

-Mike

5

HI, Mike:

Yes. I did get human-stool.qza from readytowear.

Could you please tell me how to download human-stool.qza full-length class weights'?

Thanks,

Jin

6

They are in the same location from which you downloaded the V4 class weights, look in the full_length folder.

-Mike

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