Yes, Geneious Prime can map RNA-seq reads to a genomic reference sequence using the Geneious RNA assembler (Geneious R9 onwards). 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.
Geneious also has a plugin for the Tophat RNA-seq mapper, which works with Geneious versions 7.0 and above.
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 (with or without replicates) 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 expression levels between two sample conditions you can either use the Geneious expression analysis tool or if you have replicates for each condition, use the Geneious implementation of DESeq2. These options are available under Compare Expression Levels in the Annotate and Predict menu. To compare two samples you must first run Calculate Expression levels on the reference assemblies for each sample replicate (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 run Compare Expression Levels.
Note: The Geneious de novo assembler will also assemble RNA-seq data, but be aware that the de novo 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.