Question: Deseq2 post functional annotation for metagenome
0
gravatar for anjali.kumari
7 days ago by
anjali.kumari0 wrote:

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 • 49 views
ADD COMMENTlink modified 6 days ago by Michael Love25k • written 7 days ago by anjali.kumari0

Cross-posted https://www.biostars.org/p/397969/

ADD REPLYlink written 6 days ago by ATpoint20
Answer: Deseq2 post functional annotation for metagenome
0
gravatar for Michael Love
6 days ago by
Michael Love25k
United States
Michael Love25k wrote:

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

ADD COMMENTlink written 6 days ago by Michael Love25k
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