Beginner here, what way can I use these files for generating useful plots with QIIME2?

HI folks, I have been given 4 files by my project supervisor to generate some useful plots, tables and graphs… mainly concerned with PCA plots and Alpha and Beta diversity.

Here are the file names I have been given:


I have gone through the moving pictures tutorial successfully, but cannot seem to get any results with these files using the same commands. I wouldn’t ask, but after spending hours searching for answers on the net, it seems that there is not a lot of info available concerning these file types except in this forum.

Are there any simple commands or pipelines that I could use?

Any help would be appreciated.


Hello @dvdharkin,
Welcome to the forum!
I was going to recommend the moving picture tutorial but I see that you have already tried that. Can you clarify what you mean by you can’t get any files using the moving pictures tutorial commands? What commands were you trying?
Chloe :turtle:

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Hi Chloe, I’m trying to use the files with the moving pictures tutorial by substituting my files for the ones in the tutorial buit I keep getting error messages.

For example:
“”“There was a problem with the command:
(1/1?) no such option: --m-first_sample_meta.tsv”""

when I try to run lines of code with my files.

I am in the QIIME2 environment, so not sure why the commands aren’t working.

Any suggestions?

Hi @dvdharkin, I am beginner too.

Assuming that first_feat_tab_filt.qza is equal to table.qza in Moving pictures tutorial, maybe you can try first create first_feat_tab_filt.qzv (notice the extension ended with V) with this command (it is from FeatureTable and FeatureData summaries section):

 qiime feature-table summarize \
   --i-table first_feat_tab_filt.qza \
   --o-visualization first_feat_tab_filt.qzv \
   --m-sample-metadata-file first_sample_meta.tsv

And then decide the sampling depth by visualizing it via (drag drop your qzv file). You can check Alpha and beta diversity analysis section. For starter, maybe you can choose the minimum number of reads, but I am not sure about this either :smile:

qiime diversity core-metrics-phylogenetic \
--i-phylogeny first_rooted_tree.qza \
--i-table first_feat_tab_filt.qza \
--p-sampling-depth **determined depth hre** \
--m-metadata-file first_sample_meta.tsv \
--output-dir core-metrics-results

Do similarly with qzv file inside core-metrics-results folder to view the plot. Please correct me if I am wrong.


Hi, thanks guys. I got it sorted.

It was just a case of getting used to the commands and syntax.

@Diki, yes, part of the problem was knowing where to start the tutorial with my files.

I started at the feature table section in the tutorial and it ran relatively smoothly after that.

Hope this helps anyone with similar issues.

Its great to have this forum as resource too.

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