Question: Normalization of read counts for Metagenomics data

Question

[phongphak.06]

Hi,

I'm dealing with gene abundance analysis of metagenomics data (whole-genome shotgun seq). So I've done read count by using featureCounts. Anyway. I have no idea how to normalize since there are a lot of methods use for this purpose and I also have no experience in this analysis.

So should I use the same methods as differentially expressed genes analysis of rna-seq data like RPKM, TMM or logCPM.

[phongphak.06]

This is a gene abundance of an individual sample (not compared to the other samples).

[Renesh]

Please, read this article,

http://bioinfogeek.over-blog.com/2017/09/gene-expression-units-explained-rpm-rpkm-fpkm-and-tpm.html

Answer 1

[colindaven]

This is a complex topic. You can do GC normalization, library size normalization and so on.

Here is a good paper on the topic which may help.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165015