Loci under selection

[Moises Bernal]

Hi all, 

I am doing genome scans to find loci under selection between species of coral reef fish. To do this, I use the "populations" program to generate a Structure file for SNPs found between my species. I use PGDspider to translate that Structure output into Bayescan format, in order to run the mentioned selection analysis. Depending on the parameters I use I have found up to 7 loci under selection.  

My question is the following: How can I trace back the loci under selection to the actual sequence of the loci in Stacks? The Bayescan output numbers the loci in ascending order (1, 2, 3, N) and keeps the same order as the Structure output file. Thus, it is possible to know in the Structure file which loci is under selection. Yet, I have no clue how to link that Structure allele frequency to the actual loci in Stacks. That would be very informative to see if, by chance, we can identify the loci under selection. 

any ideas help, thanks in advance for any help. 

saludos, 

[Julian Catchen]

Hi,

Stacks will output each locus to Structure using its catalog ID. You should be
able to track any particular SNP back according to its catalog locus and view
that locus in the web interface. In the Structure file, catalog loci are listed
as the column IDs in the second row, while each row then corresponds to the
value of that catalog locus in a particular individual sample.

You shouldn't try to link a locus back from Structure or Bayescan based on its
allele frequency.

Best,

julian

[nadia]

Moises Bernal,

May I know the population command you ran for the analysis? especially regarding the filter to put be put on…

Thanks

[Moises Bernal]

Hi Nadia the analysis was made using the program BayeScan, it is not part of the Stacks pipeline. 

To use that program you can export your SNP matrix as a structure file format and translated it to Bayescan format using PGDSpider. 

cheers 

--
Stacks website: http://creskolab.uoregon.edu/stacks/
---
You received this message because you are subscribed to a topic in the Google Groups "Stacks" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/stacks-users/LPsX1ganxPA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to stacks-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Moisés A. Bernal
PhD Candidate, UTMSI

California Academy of Sciences

55 Music Concourse Dr
San Francisco, CA 

94118