In Geneious R9 we have introduced the 'Geneious for RNA seq' assembler for mapping RNA-seq reads to a reference sequence. This assembler can discover novel introns and map ends of reads correctly around these novel introns, or it can map reads to introns via CDS, mRNA or junction annotations on your reference sequence. This assembler will also discover fusion genes.
For Geneious R8 and earlier you can also use the Geneious Map to reference assembler to assemble RNA-seq data but you will need to increase the maximum gap size and maximum allowed gaps per read under the Advanced options to account for the likely size of your introns. Geneious also has a plugin for the Tophat RNA-seq mapper, which works with Geneious versions 7.0 and above.
The Geneious de novo assembler will also assemble RNA-seq data, but be aware that the assembler is not specifically designed to handle transcriptome data and won’t take alternative splicing and differences in coverage levels into account when producing an assembly.
Geneious R8 and later contains tools for digital gene expression analysis, allowing you to calculate normalized expression measures TPM, RPKM and FPKM on reference mappings of individual samples, and to compare values between two samples to find differentially expressed genes. To calculate TPM, RPKM and FPKM for individual samples, select your reference assembly and go to "Calculate Expression Levels" under the Annotate and Predict menu. The results are displayed as a heat map annotation track on the reference sequence. To compare two samples you must first run Calculate Expression levels on the reference assemblies for each sample (which must have the same reference sequence), then click Save to apply the results track to the reference sequence document. Then select the reference sequence and go to "Compare Expression Levels" under the Annotate and Predict menu. For more information, please see the Geneious User Manual (PDF or online).
post updated Nov 2015