A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples

Table 3 Summary of the decisions in exome capture-based protocols

Protocols	Parameters	Pros	Cons
Exome Panels	Illumina	Highest sense rate	Lowest target enrichment
	Agilent	Most cited panel design	Highest rRNA contamination
	NardPrep	Highest capture efficiency	None
Library Preparation	Strand-Specific	Increased genome mapping rate	Reduced transcripts identification
Library Preparation	Multiplexing	Comparable and low-cost libraries	Pilot study needed before experiments
Sequencing	Illumina	High quality reads	High duplication rate
	DNBSEQ	Flexibility of throughputs and read lengths	None
	Shorter Reads	Increased reference alignment	Elevated sequencing cost

ISSN: 1471-2164