Deseq2 post functional annotation for metagenome
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@anjalikumari-21851
Last seen 2.0 years ago

Hi All,

I would like to do differential abundance analysis using DESeq2 for shotgun metagenome data. I have used the MOCAT2 for generating functional annotations. Eg: For ARDB database, Do we need to consider the "unassigned reads" (reads which didn't get assigned to any of the ARDB categories - which is around 99% of the reads) for DESeq2 analysis? Will "unassigned reads" impact the sizefactorestimation calculation?

deseq2 metagenome mocat • 548 views
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This is an active question in the community. Many papers use DESeq2. I am doing microbiome pathway analysis, and my KO and pathway abundances are mostly slightly bimodal, and certainly do not follow a negative binomial distribution (what the DESeq2 model is built around).

In discussions, I've had a few people suggest simply relying on non-parametric group tests. That does not work for us because we have a large number of covariates--we need to use something that works like regression or ancova. But those are dangerous with the kind of distributions I'm seeing--hence DESeq2 seems tempting because it works very hard to do proper normalization.

I have been considering PERMANOVA, which I have used for beta-diversity. But I do not know if it is appropriate for this job.

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@mikelove
Last seen 3 hours ago
United States

I don't have much experience in metagenomics analysis, maybe try posting a question for the phyloseq developers.

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