q2-phylogeny for vertebrates

[Nicholas_Bokulich]

Hi @DeannaB ,
I just want to chime in to add to @SoilRotifer 's excellent advice.

One amendment to this step:

@SoilRotifer

Then using QIIME 2 View search (upper right of visualization) or scroll through the taxonomy presented in the 12S-tax-derep-uniq.qzv file. Write down a list of IDs that you'd like to use into a text file. We'll call it seq-ids-to-keep.txt. Using the following format:

Making a text file of IDs should not be necessary — there should be programmatic ways of accomplishing the same thing, whether you want IDs that are in a feature table, or to filter based on IDs found in a taxonomy.

@DeannaB

I couldn't find a way to filter the FeatureData[Taxonomy] artifact of the reference database (12S-tax-derep-uniq.qza) prior to merging. I did find this post on the topic.

The RESCRIPt plugin (not currently installed as part of QIIME 2, but installation instructions are available on the forum) has an action to filter a taxonomy based on a list of IDs or search term. See this tutorial:

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt - #7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Ben…

RESCRIPt, by the way, could also be used to programmatically download reference sequences and taxonomies directly from NCBI based on an entrez search query... so that could also be an option if you only want to grab a limited number of accessions vs. all of mitofish.

Good luck!