A researcher at University of California Davis questions the basic assumption that deeper sequencing is better. They utilized the Shannon Entropy approach to estimate the information contained within a transcriptomics experiment and tested the ability of shallow RNA-seq to capture the majority of this information. Shannon Entropy is a sensitive tool used to estimate the diversity of a system.
Their analysis showed that it was possible to capture nearly all of the network or genomic information present in a variety of transcriptomics experiments using a subset of the most abundant 5000 transcripts or less within any given sample.
Given that most modern sequencing technologies are conservatively giving 100 million reads per lane, this would suggest that multiplexing of up to several hundred samples per lane would still allow for over 90% of the transcriptomic information content to be obtained in each sample.
- Kliebenstein DJ. (2012) Exploring the shallow end; estimating information content in transcriptomics studies. Front Plant Sci. 3:213. Epub 2012 Sep 10. [article]