Has anyone used chloroplast "contaminants" to do host phylogeography?

Looks like I was using 2019.7. My fault for not installing the newest version!

I’m trying to use RESCRIPt to create a reference database of 16S plastid sequences as described in my previous conversation here with @Nicholas_Bokulich.

I’m a little unsure of how to use this approach to only get a database of plastids. I feel like it would make sense to start by only downloading plastid sequences, but I’m having some difficulty using the --p-query option to get what I am looking for.

Thanks for any additional help!

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