Question: Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)
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gravatar for jfo
3.0 years ago by
jfo10
jfo10 wrote:

Hello everyone,

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.

Questions:

  1. What program/s can be used for this task?

  2. 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.

Thanks!

snp transcriptomics • 1.2k views
ADD COMMENTlink written 3.0 years ago by jfo10

popoolation2 https://sourceforge.net/projects/popoolation2/ seems to be good. My colleague used this and is quite happy with it. Pooled data is never ideal for popgen analysis as accurate estimation or allele frequency is a problem but it is still acceptable in papers particularly if the major finding is further supported by downstream analysis like Sanger sequencing. If allele frequency estimation is acceptable then Fst should also be acceptable.

ADD REPLYlink written 3.0 years ago by microfuge1.2k

Hi microfuge!

Thanks for the reply! Do you happen to know a software that can compute for hudson's Fst per SNP? Thanks again!

ADD REPLYlink written 3.0 years ago by jfo10
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