Deseq2 post functional annotation for metagenome
1
1
Entering edit mode
@anjalikumari-21851
Last seen 5.2 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 • 1.7k views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode
@mikelove
Last seen 12 hours ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 532 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6