To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. In our paper we proposed also methods to identify putatively problematic transcripts.
Konczal, M., Koteja, P., Stuglik, M. T., Radwan, J. and Babik, W. (2014), Accuracy of allele frequency estimation using pooled RNA-Seq. Molecular Ecology Resources. doi: 10.1111/1755-0998.12186
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