Qiita context for 18S

[chahoos]

Hi all,

I have a quick question about the Qiita contexts that are available through the clawback plugin/redbiom.

qiime clawback summarize-Qiita-metadata-category-and-contexts
--p-category "sample_type"
--o-visualization sample_type_qiita.qzv

The above command in the clawback plugin shows that only 16S and a few shotgun contexts are available.

This tutorial (Querying for public microbiome data in Qiita using redbiom) however shows that there was at least an 18S context in Qiitta at one point (Pick_closed-reference_OTUs-Greengenes-illumina-18S-v9-150nt-bd7d4d). Were the contexts updated since June 2018 when this tutorial was written?

I want train a naive bayes classifier for 18S sequences weighted for Eukaryotes from freshwater sources. I've used qiime feature-classifier extract reads and fit-classifier-naive-bayes to obtain the unweighted classifier and I've used redbiom search metadata to get a list of sample IDs but I don't think I can use any of the available Qiita contexts to obtain the appropriate 18S ASVs?

Thanks for your help.

[wasade (Daniel McDonald)]

Dear @chahoos,

Sorry for the delay in reply. During refinement of redbiom cache loading, we had limited it briefly to 16S and taxonomic WGS data. ITS and 18S are now available again although the context names may have changed since before,

Best,
Daniel

[chahoos]

Ah that's great. I see them now too. Thanks!