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4 weeks ago
I'm a beginner in bioinformatics, I just wanted to know if its possible to perform GWAS to identify SNP which is deferentially expressed in one population compared to other population. Any response is appreciated, Thank you for responding in advance
If its possible, what's the number of data would be sufficient to obtain a statistically significant results. I don't have any background in bioinfomatics, if I'm wrong please feel free to correct me.
GWAS are typically used to look at phenotypic traits associated with genomic variation. To my knowledge, this isn't an appropriate methodology to compare SNP variation among populations. Maybe something like STRUCTURE might be more appropriate, but it's hard to tell from your question.
Also, SNPs aren't differentially expressed. They can segregate by population. Transcripts containing variants like SNPs may be differentially expressed.
Regarding how much data is needed. Check the literature and find similar studies to what you are aiming to do. This will inform your decision of appropriate methods and data requirements. If you're still unsure, post again with your methodology outline, estimate of data, and justification and we will provide opinions.