Dada2: assignTaxonomy and addSpecies

1 
Please update the SILVA 138 dataset for me on the galaxy.org server.
Thank you.
2

Hi @Oanh_Ki_u

This is a great request and it does seem that these could use an update.

I’ve opened an issue ticket here for the IUC to process the request.This will likely take some time, but let’s see what they report back as comments on the ticket.

Meanwhile, you don’t have to wait! Instead of using a built-in index, you can load up the database fasta into your history, then select it on the tool form.

The data source would be from here:

Steps

  1. You can copy the URL for the file you want and paste it into the Upload tool using all defaults. The file should have the datatype format of fasta.gz automatically assigned once fully loaded.
  2. Select that new dataset from the history on the dada2: assignTaxonomy and addSpecies tool form.

dada2-select-reference-from-history
dada2-select-reference-from-history1546×744 53.7 KB

Hope this helps but please let us know if you have any questions! :slight_smile:

3

Hello,

I am having trouble with the DADA2 → phyloseq workflow. I successfully generated both the sequence table and taxonomy table from the DADA2 pipeline. However, when I try to create a phyloseq object using the “phyloseq object” tool, the dropdown menus for selecting the sequence table and taxonomy table are empty.

These files should appear in the dropdown list, but nothing shows up, and I cannot proceed with creating the phyloseq object.

What could be causing this issue, and how can I fix it?

Thank you.

4

Hello,

I am having trouble with the DADA2 → phyloseq workflow. I successfully generated both the sequence table and taxonomy table from the DADA2 pipeline. However, when I try to create a phyloseq object using the “phyloseq object” tool, the dropdown menus for selecting the sequence table and taxonomy table are empty.

These files should appear in the dropdown list, but nothing shows up, and I cannot proceed with creating the phyloseq object.

What could be causing this issue, and how can I fix it?

Thank you.

5

Hi @kalip

Let’s keep everything together for context.

Would you please explain a bit more about the data artifacts involved? I’m curious about the metadata and the reference you used. A shared history will show some of this but a screenshot with what you are seeing, and the parameters set on the form will be relevant too.

Thanks! :slight_smile: