rarefaction and diversity followed by metphlan2

[Jesse]

Hi, 

1) Is there a way to rarefy metaphlan2 results?

2) I want to calculate alpha and beta diversity based on metaphlan2.

1. Can you suggest a way/tool to calculate diversity based on metaphlan2 outputs?
2. Some of the diversity measurements based on absolute counts. I understand it might not be straightforward but is there a way to get estimation of absolute counts?

Many thanks!

[Francesco Beghini]

Hi Jesse,

for rarefying MetaPhlAn2 results you should rarefy the input metagenomes to the desired depth using e.g. seqtk.

You can perform ecological analyses starting from the output profiling file and then filtering at the species level. You can than use Python with SciKit-bio (http://scikit-bio.org/) or R with Phyloseq (https://joey711.github.io/phyloseq/) or Vegan to analyse the data.

Phyloseq has a nice tutorial (https://joey711.github.io/phyloseq/import-data.html) for analysing microbiome results.

Hoping this helps you,

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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[Jesse]

Thanks!

Any way that rarefaction can be done on the bam file (I believe it depends on whether the bam includes only mapped reads or both mapped and unmapped).

On Tuesday, September 10, 2019 at 12:18:14 AM UTC+3, Francesco Beghini wrote:

Hi Jesse,

for rarefying MetaPhlAn2 results you should rarefy the input metagenomes to the desired depth using e.g. seqtk.

You can perform ecological analyses starting from the output profiling file and then filtering at the species level. You can than use Python with SciKit-bio (http://scikit-bio.org/) or R with Phyloseq (https://joey711.github.io/phyloseq/) or Vegan to analyse the data.

Phyloseq has a nice tutorial (https://joey711.github.io/phyloseq/import-data.html) for analysing microbiome results.

Hoping this helps you,

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

On Sun, Sep 8, 2019 at 8:30 PM Jesse <yip...@walla.com> wrote:

Hi, 

1) Is there a way to rarefy metaphlan2 results?

2) I want to calculate alpha and beta diversity based on metaphlan2.

1. Can you suggest a way/tool to calculate diversity based on metaphlan2 outputs?
2. Some of the diversity measurements based on absolute counts. I understand it might not be straightforward but is there a way to get estimation of absolute counts?

Many thanks!

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