Methods of transcriptome analysis2
| Name of technology | Technique | Advantages | Disadvantages |
| Next-generation sequencing; RNA seq | RNA is fragmented, sequenced and compared against a reference sequence. | More comprehensive and good coverage. Allows quantification of transcripts and broad discovery, no prior knowledge needed and alternative splicing isoforms viewable. | Huge amount of information generated. |
| Microarray | Sample hybridises with probes for specific transcripts fixed to array and determines if sequence present in sample. | Cheap, comprehensive coverage and allows quantification of transcripts. | Not sensitive—unable to detect transcripts that are not in the probe set. |
| Real-time quantitative PCR | Amplification of targeted RNA sequences | Sensitive. Allows quantification of transcripts. Useful for validation of other methods. | Limited scope and coverage. |