Question: Diversity analysis after metaphlan2
0
gravatar for biobiu
8 months ago by
biobiu110
United States
biobiu110 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 • 420 views
ADD COMMENTlink modified 5 months ago by theglobetrotter7830 • written 8 months ago by biobiu110
0
gravatar for DriesB
5 months ago by
DriesB30
Leiden, The Netherlands
DriesB30 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 5 months ago • written 5 months ago by DriesB30

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 5 months ago by DriesB30
0
gravatar for theglobetrotter78
5 months ago by
theglobetrotter7830 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 5 months ago by theglobetrotter7830
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1221 users visited in the last hour