How to make a Cladogram with QIIME 2 data?

[Jacob95]

Hello

I am new to QIIME2.
I just finished the QIIME2 tutorial.

There is one thing that I could not get the correct answer by myself.

I want to make the Cladogram with QIIME 2 data on the LeFSe environment.
I have found several suggestions and I have tried them.
But I could not get the result that I want.
There may be some errors...

Can you walk me through the process of making the data can be used in the LeFSe environment?

FWI, I think below is one of the solutions, but I can't understand how to do it.

1. Are my QIIME 2 data (.qza) compatible with dokdo commands?
2. I am curious about the next step after installing dokdo.

Thank you so much.

[SoilRotifer (Mike Robeson)]

Hi @Jacob95, welcome to ! Hopefully, we can get you running LEfSe.

Regarding the post:

Weird cladogram

Hi @Barandouzi, This looks like LEfSe output. If it is, then this is not a true cladogram, despite name of the function. It is merely a dendrogram based on taxonomic ranks, were each node is a taxonomic level. If you do not have | separating the ranks, then you're only ever going to see this "star" cladogram. Where each tip is a unique full taxonomy string. I'd recommend installing dokdo into your QIIME 2 environment and then run the prepare-lefse command. Then upload to LEfSe Galaxy.

@Jacob95

Are my QIIME 2 data (.qza) compatible with dokdo commands?

If you read the dokdo documentation and the tutorials you'll see that dokdo uses the QIIME 2 API and is intended to be used with QIIME 2.

@Jacob95

I am curious about the next step after installing dokdo.

Again, everything you need to know is in the dokdo documentation. Here are the installation instructions. Though it is much easier to simply install like this:

conda activate qiime2-2022.8
pip install git+https://github.com/sbslee/dokdo
dokdo --help

Then run the prepare-lefse command as described here.

[Jacob95]

Thank you so much!
It worked.
But the result was slightly different from what I have expected so I will make some measurements on my raw data before re-running LEfSe.

Have a good day!