I am analyzing Shotgun Metagenomic Sequencing and 16S sequencing data. Shotgun Metagenomic Sequencing, sequences all given genomic DNA from a sample, whereas, 16S sequencing only targets 16S rRNA genes.
I have both measurements for more than 80 subjects.
My experience shows that integrating these data (following a correct data integration workflow) yields more stable phenotypes.
Let me know your thoughts and ideas? Do you think integrating complementary datasets is a good idea, especially Metagenomic Sequencing and 16S sequencing data?
I think if you just need to identify samples on Genus levels then 16S would be fine, if you need species level identification, then shotgun sequencing would be great. So if you go with shotgun sequencing there is no need to combine the 16S data with the shotgun sequencing data, since the shotgun will already include all genus and species present in sample.
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