This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies, including short read mapping, exon-exon splice junction detection, gene or isoform expression quantification, differential expression analysis and transcriptome reconstruction.
Table 1 Tools for short read mapping
Table 2 A list of software for splice junction detection
Table 3 Software for gene or isoform expression quantification
Table 4 Available tools for differential expression analysis
Table 5 Transcriptome reconstruction tools
- Chen G, Wang C, Shi T. (2011) Overview of available methods for diverse RNA-Seq data analyses. Sci China Life Sci 54(12), 1121-28. [article]
Previous reviews covering RNA-Seq data analysis strategies and tools: