Hello everyone,
I have a question related to using SNPs as markers of population heterogeneity.
We have four fly strains who are supposed to have the same genetic background. To check if this is the case, we performed SNP calling on the whole transcriptome, on the four sample for each of four strain. Then we compared four samples - one from each strain - using Venn diagram, and the results were discouraging since only half of SNPs (~10000) was shared by all four strains, and the rest were strain-specific of shared by three or four strains (attached below). Then we took four samples for one strain and did the same, and the picture was quite similar (attached below). To my opinion, the fact that intra-strain variability is the same as inter-strain indicates that the background in all strains is moreless the same. The question is are there any tools which would statistically reinforce this observation?
I have found some of R packages for population genetics (DEMEtics, popgen, genetics, pegas) working with SNP, but they need allele frequencies which are barely absent in my case. Another constraint (or not?) is that one sample in my experiment contains pooled RNA from 60 flies whereas the listed R tools work with one individual as a sample.
I would highly appreciate any advice!
Best regards,
Nina.
I have a question related to using SNPs as markers of population heterogeneity.
We have four fly strains who are supposed to have the same genetic background. To check if this is the case, we performed SNP calling on the whole transcriptome, on the four sample for each of four strain. Then we compared four samples - one from each strain - using Venn diagram, and the results were discouraging since only half of SNPs (~10000) was shared by all four strains, and the rest were strain-specific of shared by three or four strains (attached below). Then we took four samples for one strain and did the same, and the picture was quite similar (attached below). To my opinion, the fact that intra-strain variability is the same as inter-strain indicates that the background in all strains is moreless the same. The question is are there any tools which would statistically reinforce this observation?
I have found some of R packages for population genetics (DEMEtics, popgen, genetics, pegas) working with SNP, but they need allele frequencies which are barely absent in my case. Another constraint (or not?) is that one sample in my experiment contains pooled RNA from 60 flies whereas the listed R tools work with one individual as a sample.
I would highly appreciate any advice!
Best regards,
Nina.
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