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Old 09-26-2019, 09:01 AM   #1
dacotahm
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Location: ND, USA

Join Date: Oct 2011
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Default How to estimate genetic variation in a population with RNASeq data?

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?
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