I have performed an SNP analysis of the whole transciptome data. Now I have received Fst values ranging from 0.3 to 0.9. Can I consider the SNPs with Fst value above 0.5?
Fst is usually not a criterion used for SNP filtering. It indicates how heterozygosity varies in subpopulations comparing with total population. Fst is very important for analysis of population structure. Of course, depending on your scientific problem, you may want to select SNPs from particular ranges of Fst values later, for example higher Fst indicates higher specificity of marker to a subpopulation. But initially all SNPs should be examined regardless their Fst.
Definitively, FST is not a statistical proof of significance. What are you trying to solve with that analysis?
It depends on the distribution of your Fst values and is also up to you to consider top %1 or 0.01% of Fst values as significant as suggested in the literature. Of course this is for selection signaure studies, and I do not have sufficient information about transcriptome data. It seems to be a good idea to standardize your Fst values (i.e. mean~0 and SD~1) by [Fst(i)-Mean(Fst)]/SD(Fst), and then consider top 1% of Fst values as significant.
If you are looking for outlier loci or selection signals, as Mario Barbato and Mohammad Ghoreishifar had suggested, I may recommend you to analyze your data with Bayescan software.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA