Question: Normalization of read counts for Metagenomics data
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.
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colindaven
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phongphak.06 •
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phongphak.06 •
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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
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This is a gene abundance of an individual sample (not compared to the other samples).
Please, read this article,
http://bioinfogeek.over-blog.com/2017/09/gene-expression-units-explained-rpm-rpkm-fpkm-and-tpm.html