To perform a RNAseq analisys with a reference genome, you have to follow the next steps:

Open RNAseq tool of the GPRO suite.
Go to Transcripts Protocols > Step-by-Step Mode > Tophat/Hisat & Cufflinks Protocol.
Do the quality analysis. To do this, go to Preprocessing > Quality Analysis > FASTQC. There, use your raw FASTQ files as input.
After the quality analysis, you have to perform the preprocessing step, so you have to click on Preprocessing > Trimming & Cleaning and select the software you want to use. If the quality analysis indicates you that there are adapters in your samples, you have to use CUTADAPT to remove them. Next, use PRINSEQ to preprocess your FASTQ files. Depending on the quality analysis, you have to use a set of parameters or another, but there are some options that are normally used such as -trim_ns_left, -trim_ns_right, -trim_qual_right, -min_len, -max_len, -min_qual_mean and -ns_max_p.
Once you have preprocessed your FASTQ files, it's time to map your reads against the reference genome using Tophat. To access to Tophat, click on Mapping > Tophat. Here, you have to provide an index file or a reference genome if you don't have it, your preprocessed FASTQ files and a GTF file with the annotation. It's recommendable to build a new transcriptome clicking on "Build New Transcriptome" option.
After you get the BAM files from the mapping step, you have to run Cufflinks. To access to Cufflinks go to Transcriptome Assembly > Cufflinks. Here, drag your BAM files to the corresponding dialog, introduce the GTF file containing the annotation and the reference genome inside two options: Reference sequences [seq_fasta] (Cuffmerge option) and -b option (frag-bias-correct [genome.fa]). If you only want to obtain the results for the known transcripts, click on "Do not Assemble novel transcripts".
Finally, you can perform the differential expression analysis using Cufflinks which is located in Differential Expression Test > Cuffdiff. You just have to supply the GTF file, your BAM files, sample group, the comparison you want to do and the reference genome in the -b option (Reference genome for bias correct).

For further information, you can consult the https://biotechvana.com/gpro/tool/rnaseq/manual/overview