Alpha and Beta Diversity Explanations and Commands https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282

[Rashmi_Ira]

Hello

I want to check the number of OTUs/ASVs per sample.
For that, I tried to work with the command

@Stephanieorch

qiime diversity alpha-phylogenetic \
  --i-table table.qza \
  --i-phylogeny rooted-tree.qza \
  --p-metric faith_pd \
  --o-alpha-diversity faith_pd_vector.qza

or

@Stephanieorch

qiime diversity alpha \
  --i-table table.qza \
  --p-metric observed_otus \
  --o-alpha-diversity observed_otus_vector.qza

But I am not sure whether I am going right or not.

Also, I have generated the qza file, but now I want to visualize those files. So, how can I visualize them? Any particular command or code???

Another query: how do **alpha and alpha-phylogenetic methods** and alpha diversity group significance vary?

@Stephanieorch

alpha and alpha-phylogenetic methods

Any comments or suggestions will be appreciated!

Thanks and Regards,
Rashmi Ira

[jphagen (Johannah Hagen)]

Hi @Rashmi_Ira,
Lets start with this question:

@Rashmi_Ira

Another query: how do **alpha and alpha-phylogenetic methods** and alpha diversity group significance vary?

Alpha and alpha-phylogenetic methods compute an alpha diversity metric for the samples in your feature table. While alpha group significance will compare groups of alpha diversity values.

You ran qiime diversity alpha-phylogenetic and your next step is to run qiime diversity alpha-group-significance using your output .qza, this will create a visualization and calculate statistics for the metric you calculated in your first step.

Once you have your .qzv you can use qiime tools view from the command line or https://view.qiime2.org/ to view your artifact.

Hopefully this is helpful to you!
-Hannah

[Rashmi_Ira]

Hi @jphagen ,

First of all, thank you so much for your response.

There's a follow-up question, if we use the qza file obtained from the alpha-diversity method, which does not deal with grouping then how can we use "

qiime diversity alpha-group-significance

" command for visualization?

Because the results from group significance I have analyzed earlier, in which we get the significant or non-significant value based on the groups but in my case I just want to know the number of OTUs or unique features per sample!!!
Please, let me know if I'm using the right command for that or need to use another method.

Regards,
Rashmi

[jphagen (Johannah Hagen)]

Hi @Rashmi_Ira,
There is no command to view your OTU in Qiime2, but you can unzip your .qza artifact, find the data folder and open the alpha-diversity.tsv this will have your OTU counts you calculated in the alpha diversity step.
I hope this is helpful to you!
-Hannah

[Rashmi_Ira]

Dear @jphagen

Yup it worked for me to extract the count per sample.

Thank you so much.

Best Regards,
Rashmi