Hello from beautiful Santa Cruz, CA!
I am interested in identifying variable expression levels as well as sequence polymorphism between conspecifics in different environments all in one fell swoop and it seems that RNA-seq is the right tool for this mission. However it seems that detecting variable expression levels requires ample coverage for sensitivity purposes while detecting polymorphisms (i.e. SNPs) doesn't require as much depth. Is it safe to assume that if you obtain sufficient coverage to detect variable expression that you will have the power to detect polymophisms? Are there any models for estimating sufficient sequencing depth to achieve the desired power to detect expression differences? I am working with teleost fishes with ~1Gb genome.
Any insight into the pros and cons of RNA-seq library preps (price and efficacy) would also be greatly appreciated!
Cheers,
Gary
I am interested in identifying variable expression levels as well as sequence polymorphism between conspecifics in different environments all in one fell swoop and it seems that RNA-seq is the right tool for this mission. However it seems that detecting variable expression levels requires ample coverage for sensitivity purposes while detecting polymorphisms (i.e. SNPs) doesn't require as much depth. Is it safe to assume that if you obtain sufficient coverage to detect variable expression that you will have the power to detect polymophisms? Are there any models for estimating sufficient sequencing depth to achieve the desired power to detect expression differences? I am working with teleost fishes with ~1Gb genome.
Any insight into the pros and cons of RNA-seq library preps (price and efficacy) would also be greatly appreciated!
Cheers,
Gary
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