Question: DESeq2 post functional annotation for metagenomics
0
gravatar for anjali.kumari
8 months 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?

metagenomics deseq2 mocat2 • 295 views
ADD COMMENTlink written 8 months ago by anjali.kumari0

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.

ADD REPLYlink written 8 months ago by ATpoint34k
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