RNA-seq 

Next-generation cDNA sequencing (RNA-seq) makes it possible to sequence complete transcriptomes in almost any population or tissue. Although often used to measure gene expression\, RNA-seq has also been used to discover tens to hundreds of thousands of SNPs in human cell lines\, bovine milk and black cottonwood. This can be done at similar costs to the restriction-enzyme-based methods\, and is more likely to detect functional (for example\, disease-related) SNPs. However\, inferring genotypes from expression data can be challenging\, and normalizing the range of dynamic expression may be desirable. Alternative transcripts can also make it difficult to infer genotypes\, particularly when no reference genome is available\, as de novo transcriptome assembly remains daunting. (Davey 2011)