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How to get ITS amplicon environmental samples #102

Closed hotblast closed 2 years ago

hotblast commented 4 years ago

My goal is to get the community profile of all ITS studies that have GPS location. I searched "redbiom search metadata ITS | redbiom summarize samples --category sample_type | head". All i got is 48 control blank.

Then I searched the https://qiita.ucsd.edu/study/list/ site , Among 543 entries in Qiita Public Studies, there are 19 studies having ITS in the Preparation Data Types field.

After I got these 19 qiita_study_id, I was trying to get their sample data in BIOM file.  I used the following command.

redbiom search metadata "where qiita_study_id == 2020" | redbiom fetch samples --context $CTX --output study.biom

As I expected, I didn't get anything back, since I don't have CTX for ITS. Any suggestions on this?

hotblast commented 4 years ago

Updated: redbiom is only indexing 16S; thus, I can not find actual ITS samples using Redbox search.

wasade commented 4 years ago

That's correct, at the moment we're only indexing 16S. The preparation information for ITS and 18S is not nearly as uniform right now, so the contexts are not well defined.