I have a RNA-seq data for three populations: pooled individuals with at least n = 40 per library; two libraries each population (a total of 6 lib); around 40M PE reads per library).
Objective: Get highest ranking SNPs using their Fst values to be used for SNP genotyping and pop gen analysis.
I have run Popoolation2 and got the Fst values for each. However, I've got 3 Fst values: p1 vs p2, p2 vs p3, and p1 vs p3.
If getting their average is not recommended, how should I compute for the "overall" Fst value for that SNP locus? Or shouId just use the p1 vs p2 Fst value (as in one of the Popoolation2 tutorial materials) to infer ranking?
Any suggestions on a more appropriate software to use (if there is any)?
Any help regarding my query or anything about the design will be much appreciated. Thanks!