training the classifier

[dr.deepakkukkar (Deepak Kukkar)]

Hi QIIME2 team, I want to know about what is training the classifier in QIIME2? Why it is required and what are the reference sequences and the corresponding taxonomic classifications under this classifier? Thanks for your help. Deepak

[SoilRotifer (Mike Robeson)]

Hi @dr.deepakkukkar,

You can read more about taxonomic classification through this overview, and the tutorial for more information. Here is an example use case from the Cancer Microbiome Intervention tutorial.

We are currently restructuring how we provide premade reference data. Mainly 16S & 18S rRNA marker gene data. Anyway, you can find them here.

You can also use the RESCRIPt plugin, (now part of QIIME 2) to construct and curate your own reference database for any marker gene.

[dr.deepakkukkar (Deepak Kukkar)]

Hi Mike, Thank you so much for your prompt replies. I will go through the suggested files and tutorials for improving my understanding about this topic.

Best regards,

Deepak

[dr.deepakkukkar (Deepak Kukkar)]

Hi Mike,

I again have some queries. I did the analysis of my samples using q2 pipeline.

1] What should be the ideal quality score for the samples being analysed after demultiplexing of the paired end sequences?
2] How to read the interactive quality plot?
3] How to validate the feature table and what are the criteria for the validation of the feature table?

Thanks and regards,

Deepak

[lizgehret]

Hi @dr.deepakkukkar,

I'd recommend going through our Moving Pictures tutorial - this will go over examination of an interactive quality plot and feature table analysis. There are also many great past threads on the forum that discuss your exact questions

Cheers

[dr.deepakkukkar (Deepak Kukkar)]

Thank you much @lizgehret for your feedback. I have already completed the moving pictures tutorial. Anyhow, I will go through the past threads on this forum for more information.

Best regards,

Deepak