We have done next generation sequencing for 16S rRNA for gut microbiota for cases (n=20) vs. controls (n=20). I would like to know how can we calculate relative abundance manually for cases vs. controls. I have read counts and OTUs for both the groups. Kindly suggest me.
Thank you.
To get relative abundances manually from the absolute ones, for each sample you need to divide each OTU's count from this sample by the sum of all OTU counts in this given sample (Python, R, Excel or analogs).
As an alternative, you can import read counts as a feature table and OTUs as representative sequences into the Qiime2 (or use your raw data to recreate it in Qiime2) and perform this task and many others there.
After the construction of OTU, I believe the QIIME2 might help you. You can find out more information at https://www.nature.com/articles/s41587-019-0209-9
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