Regarding the OTUs and Graphlan

1

Hi all.
Hope you are well and doing good!
I have successfully run Metaphlan on my datasets,
there is my history.
Galaxy | Europe
Although I have got the relative abundance, but I want the taxonomic analysis in terms of OTUs. (so which tool I can use),
Secondly, I want to know a tool wherein I can combine all the Graphlan results into a single plot, as in my case I have got plots for each sample.
thanks and Regards

2

Hi @mallamuneer123

Have you seen our tutorials? Search with the tool name. Search Tutorials

3

Hi@ jennaj
Thank you so much for your reply
I searched but am not able to choose one, kindly suggest which one to choose
Thanks and regards

4

Hi again
I tried one but I am confused with the generated dataset
How can be the number of OTUs in decimals
like here in the attached file

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image1920×1080 483 KB

5

Hi @mallamuneer123

You’ll need to show the file in Galaxy, not a text editor please.

6

Hi @mallamuneer123;

  • Metaphlan returns relative abundance by default (if you want estimated reads, you can choose the option: Type of analysis to perform: rel_ab_w_read_stats); it does not however return OTU counts, the numbers represent the relative abundance for a given taxa level. See left column, each row represents a taxon on a specific level. You can also observe the relative abundance for a given level by looking at the Predicted taxon relative abundances at each taxo... output.
  • In terms of plotting, you can use krona and phinch to visualize multiple samples, but I think you need to merge the biome files for the input … that needs some data science, I would first need to look up.
    Best, Paul
7

Thank you so much @paulzierep
Got it, however, I have during my analysis also got a biom file.
Which I think contains the OTUs (if, I am not wrong here).
So , how can I convert the biom file into a tabular file or CSV/TSV etc.
thanks and Regards

8

biom file format does not need to contain OTUs, in case of Metaphlan it is only a different format that contains the same information as the table output. Biome format is more useful in some cases, e.g. when you want to add meta data and use it as input for tools like krona and phinch.
As an update to the previous question, you can visualize multiple Metaphlan result files using: