DESeq2 post functional annotation for metagenomics

Question

[anjali.kumari]

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?

[ATpoint]

Hello anjali.kumari!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/124511/

This is typically not recommended as it runs the risk of annoying people in both communities.