I used CRISP to call SNPs from a transcriptome data, which was a result of pooled sampling (we have to pool 10 - 60 juveniles per library to get an amenable amount of RNA). I have 3 populations with 2 libraries each. Now, I would like to compute for the Fst for individual SNPs and get the highest ranking SNPs for further pop gen analyses.
What program/s can be used for this task?
Because of the pooling effect, is this method for getting individual SNP's FST still be recommended? I am not sure if I am doing it correctly but
The organism I am interested with has no reference genome.
All your suggestions will be much appreciated.