So, I am a bit new to galaxy, i have been trying to navigate there. I have attached screenshots of the step by step process i took using the v3-v4 region, of the microbiome of the higher, middle and lower leaf samples from different treatments. Now on generating the taxa bar plot, the results clearly indicate a contamination with E.coli. I have tried so many ways to filter the chloroplasts, mitochondria and e. coli, and i have two outcomes. one they are not filtered at all. Secondly for one, they are filtered but i loose the names and only have ids. I trained my classifier, I have tried re-training it filtering the sequences but its not possible. Is it possible to reassign my qiime taxa bar plots taxa ids to names on the server? What other ways can i filter the sequences so that it doesn’t affect the alpha and beta diversity calculations?
Did you solve this? It sounds like the tool is using the IDs as a primary key and dropping the name label.
We can’t see what is inside of your artifacts, but this tool will let you inspect them. (this suggestion is from a Qiime2 author)
I wonder if you can set up the artifact metadata differently to label your artifact in a way that will preserve the information you are most interested in. The Qiime2 community might be best for this. The tools in Galaxy will work about the same as when used directly since the artifacts ignore the other kind of metadata that Galaxy usually applies to data (all the datatypes are qza or qzv).
This is the forum and it is active → User Support - QIIME 2 Forum. The won’t be interested in the Galaxy screenshots, but they will probably appreciate the views from https://view.qiime2.org. It seems like your idea to map the IDs to the name is where to start but I don’t personally know of the correct tool to use, and I’m guessing other moderators didn’t either since there wasn’t a reply here yet .. that’s why I’m suggesting to go to the experts who use this tool suite the most. Any Qiime2 tools they suggest should be in Galaxy. If they suggest other methods, there might be a way to do that in Galaxy too, it depends, and you can ask.
If you want to post back what worked, that will help others later! And if you solved this already, let us know. 
well…I did not get this solved just yet. However I reached out to the forum for assistance and we are still in discussions. I am using the qiime2 view, and that is how I get to know that I loose my taxonomic names and instead have taxonomic IDs. Additionally I figured how to filter and retain the names, starting by filtering the taxa table(qza filter table), then the bar plots and then filtering the sequences. I am not sure why and the justification, but it worked.
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