Which is the preferable method of small/microRNA analysis?
RNA-Seq yields a rich transcriptome-wide data set including information about post transcriptional mutations and their genomic context. It can reveal sequence variations in the transcripts due to alternative splicing events and provide allele-specific or isoform-specific gene expression information. Microarrays are proven gene expression analysis tools that routinely deliver results rapidly, reproducibly, and cost effectively. So there is a trade-off. While RNA-Seq provides a more comprehensive view of the transcriptome and information about sequence variants, it is more expensive and lower throughput than microarrays, and bias could be introduced during extensive sample preparation steps effecting expression data. The decision to use one method or the other depends on the specifics of your project. If you are working with a species whose genome is not well known or annotated, and your research is focused on discovery, we would recommend sequencing as the method for transcriptome profi
