Table 9. Strengths and weaknesses of different data types.

	Strengths	Weaknesses
EST	Ubiquitous	Strandedness is unreliable
	Confirmed transcripts	Low coverage
	Reveals gene structure	Uneven transcriptome sampling
	Stranded
DRS	Natively stranded	Only probes 3′ UTR end position
	Exquisite positional accuracy (±2 bp)	Cannot reveal gene structure
	Quantitative	Short reads
	No amplification
	Unbiased transcriptome sampling
RNA-seq	Easy/cheap to generate high coverage	Unstranded
	High sensitivity	Size selected (>200 bp)
	Reveals gene structure	PCR amplification step
	Unbiased transcriptome sampling	Reverse transcriptase step
	Quantitative	Sensitive to read alignment details
sRNA-seq	Sensitive only to small transcripts/exons	Unstranded
	Easy/cheap to generate high coverage	Size selected (∼20 bp)
	High sensitivity	PCR amplification step
	Reveals miRNA structure	Reverse transcriptase step
	Quantitative	Sensitive to read alignment details
		No splicing