query in alpha diversity analysis

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1

Hi
I used “qiime core-metrics-phylogenetic” method for alpha diversity analysis and got results. when i used “qiime diversity alpha” for obseved-otus metrics, the result was different from the previous one. how is it possible?

thanks in advance

2

Hi,
Did you use the same rarefied table as an input in both cases? Or you rarefied the tables in each case separately, even if you used the same depth?

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3

Hi
these are the commands which I used.
can you elaborate what a rarefied table is? because I don’t have an idea about that

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 5000
–m-metadata-file metadata.txt
–output-dir core-metrics-results
in this core-metrics-results directory, it generated all alpha and beta diversity measures

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

plots from both methods were different and statistical measures too

4

and also I used qiime diversity alpha-group-significance to visualize the results from methods.

5

Hi again!
It is recommended to rarefy the table before comparing diversity metrics.
In your first run, you rarefied the table by subsampling it to 5000 random sequences, while in the second run you used your original table. I guess it is a reason for the difference you observed.
If you repeat your second command, but this time with rarefied table from your first command (you should find it in the core-metrics-results directory), the results should be consistent.
Rarefying is used to normalize you data across samples, otherwise different amount of sequences will affect statistical analysis. Although there are some discussions about should one use rarefaction for data normalization, it is common to rarefy the table.
It is also better to use the same rarefied table for each metric, since it is randomly picking sequences to keep.

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6

Hi
now it is fine. thank you!!!

7

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