Question: Diversity analysis after metaphlan2
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gravatar for biobiu
15 months ago by
biobiu120
United States
biobiu120 wrote:

Hi, I've ran metaphlan2 on shotgun metagenomics sequencing data and want to perform diversity (alpha and beta) analysis.

Is there some tools allows calculating alpha diversity metric to each sample (like shannon), and beta-diversity metrics bewteen pairs of samples (like jaccard or bray curtis).

I undestand that some metrices requires moving to absolute counts but I know that metphlan1 had this option.

Thanks!

metagenomics • 980 views
ADD COMMENTlink modified 13 months ago by theglobetrotter7850 • written 15 months ago by biobiu120
0
gravatar for DriesB
13 months ago by
DriesB90
Leiden, The Netherlands
DriesB90 wrote:

According to MetaPhlAn2's Bitbucket, you can export as BIOM. I would expect you to be able to import that into the phyloseq package, but have not tested this yet.

ADD COMMENTlink modified 13 months ago • written 13 months ago by DriesB90

I'm also in the process of analyzing shotgun sequencing metagenomics data. Please give some input to my question here, if you have recommendations!

ADD REPLYlink written 13 months ago by DriesB90

Hi.... did you analysed your shotgun data? I need help. I am doing analysis with metaphlan.

ADD REPLYlink written 4 months ago by dpc150
0
gravatar for theglobetrotter78
13 months ago by
theglobetrotter7850 wrote:

With vegan package you can calculate different diversity metrics and perform ordination analysis as well. If you want to perform statistical analysis I would recommend metagenomeSeq.

ADD COMMENTlink written 13 months ago by theglobetrotter7850
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