I’m a new in QIIME2, and a beginner with metagenomics.
I’ve done the basic data handling in Mothur and continued to visualize the results with QIIME1. So, I have the results already!
However, now I’d like to add extra information to samples (i.e. more precise source and sampling locations) and to visualize the data based on the new information. I’ve added the new information to an old mapping file (barcoded) and trying to find a way to merge it with some existing file (imported to .qza) in QIIME2, but it just won’t work. Before going into details, I’d like to ask what would be the best way to do it? Is there a way to do it? I’ve followed the “moving pictures”-tutorial, but the success rate has remained low… Should I just get back to QIIME1
Thanks for your help!
Welcome and welcome
Short answers to your questions:
- I will need some more specific details on your data and what you are trying to do to help.
- What do you hope to accomplish?
- Where are you failing? Import? Or a particular analysis step? Please report the error message you are getting
- What format are your files in? If you have imported successfully to QIIME2, you are in great shape.
- If you have results that are ready and done, you just want to reanalyze some step with new metadata, it would probably be faster/easier to just re-run your same old QIIME1 pipeline. HOWEVER, for new analyses I would definitely recommend QIIME2 over QIIME1 so it might be worth figuring this out now if it will help future analyses. The advantages of QIIME2 are going to be in the full pipeline — including denoising methods like dada2/deblur that I don’t think are available in mothur (and know aren’t in QIIME1) — so it will be worth figuring out now since you are new to metagenomics.
In QIIME2 metadata is usually kept separate from any other information — so you are probably barking up the wrong tree.
Tell me what you are trying to merge, and the analysis you want to perform, and I can tell you the QIIME2 way of doing things.
Sorry, I need the details to help out! There is probably a way to do it, but your description is too @opaque to offer any support at this stage.
I’m still looking for the right tree to bark
My goal is to achieve similiar file as taxa-bar-plots.qzv at the end of moving pictures tutorial, i.e. being able to sort the samples based on the source or the locations.
My mothur based file is converted QIIME compatible and further to .qza, the data in it is in .biom format. Following the tutorial taxa barplot command, I get this:
qiime taxa barplot --i-table feature-table-2.qza --i-taxonomy taxonomiaa.qza --m-metadata-file Oligos_st1_add_QIIME.tsv --o-visualization taxa-bar-plots.qzv
Plugin error from taxa:
unhashable type: ‘Float64Index’
Debug info has been saved to /tmp/qiime2-q2cli-err-g_u090c0.log
No glue, what that means and how to continue…
Please see this post on that error message to see if the same applies to you.
Basically, this happens when there are no overlapping feature ids between your feature table and your taxonomy. There are a couple of things you can check: 1) make sure you aren’t providing a collapsed table as input, 2) check that your taxonomy was generated using the same rep seqs as your feature table.
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