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Hello,
I'd like to estimate the amount of diversity in an insect population so that we can determine the number of individuals to include in a future re-sequencing study. I am only looking for an estimate so we can design the future experiment with enough samples to accurately assess genetic diversity at several locations.
I have a genome and RNAseq data from 35 individuals from one location as part of another project. I'd like to use the RNAseq data to estimate diversity.
This paper assembles a transcriptome from each sampled individual, maps to a reference transcriptome made from pooling the individuals, and then calls SNPs-
https://onlinelibrary.wiley.com/doi/...111/jipb.12287
Presumably I could map the reads from each of my 35 bugs to my reference genome and do SNP calling. Does this sound legit? Do you have any advice on how I would arrive at an estimate for the number of individuals needed from each location based on the variation in this population?
I'd like to estimate the amount of diversity in an insect population so that we can determine the number of individuals to include in a future re-sequencing study. I am only looking for an estimate so we can design the future experiment with enough samples to accurately assess genetic diversity at several locations.
I have a genome and RNAseq data from 35 individuals from one location as part of another project. I'd like to use the RNAseq data to estimate diversity.
This paper assembles a transcriptome from each sampled individual, maps to a reference transcriptome made from pooling the individuals, and then calls SNPs-
https://onlinelibrary.wiley.com/doi/...111/jipb.12287
Presumably I could map the reads from each of my 35 bugs to my reference genome and do SNP calling. Does this sound legit? Do you have any advice on how I would arrive at an estimate for the number of individuals needed from each location based on the variation in this population?