Entering edit mode
5.1 years ago
jeccy.J
▴
60
We have done a large scale shotgun metagenome over 100 samples and analysed using metaphlan2. Can anybody help me out how to perform a Rarefaction analysis of metaphal2 output, as i can did not see anything motioned about Rarefaction on metaphaln web page. In case of amplicon we can subsample the reads and perform the analysis but what should we do in shotgun metagenome sequencing?
Export the output to biom and import into MEGAN. MEGAN can do rarefaction analysis, alpha and beta diversities. Qiime2/Qiime can also import biom files and do the analysis.
Hi cpad0112!!! Can I do the rarefaction analysis of shotgun sequences with MEGAN?
we did it with 16s with megan. But due to licensing issues, we shifted to qiime2 pipeline. If you are new, you can follow this protocol (galaxy and mothur): https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
Hi cpad0112!!! Can I do the rarefaction analysis of shotgun sequences with MEGAN? I have shotgun metagenome sequence analysed by MetaPhlAn.
Thanks, DC7