Entering edit mode
6.4 years ago
zizigolu
★
4.3k
Hi,
I was given PLINK binary files of 16SrRNA from 50 individuals. Firstly, I was thinking this is genotypes of 16SrRNA genes. Now, I think this is the genotypes of these 50 individual based on 16SrRNA variations in their gut. However I am not sure I am right now. I was given a phenotype file too, is my file an OTU file? If so I am right that bed/bim/fam files come from genotyping of 16SrRNA in 50 individuals and I need phenotype file (screenshot that I think is an OTU) for correlation analysis between taxon and human variants. Please correct me if I am wrong again.
https://www.imageupload.co.uk/image/E42S
Thank you
Plink binary file come from genotyped individuals and the phenotype file is the same OTU
My suspicion is that the reason you have not received any answers to this is because the task you have been given is not well defined/explained in your post. What do you mean by 16S rRNA of 50 individuals? That is a prokaryotic gene. I assume 50 individuals you are referring to are human (or some other animal)?
I am sorry, you are all right. Exactly as the last year challenge I was asked a too new practical question and when they sent the file, they told this is "16S rRNA of 50 individuals" in plink binary and phenotypes file. I got confused, until I read somewhere the phenotypes file is OTU table and genotypes is from individuals not from microbiome in their bodies.
So task is to find correlation (if any) between genotype of individual <--> phenotype of individual <--> their microbiome?
Thank you, exactly. They asked to find the genes in these individual that likely associate with microbiota diversity in their bodies. For this I think I should first calculate alpha-beta diversity from OUT file I then calculate the correlation of genotypes with close and inheritable bacterial taxa. I am with windows the challenge is do everything without any possibility of Linux commands.