You will need to clarify what you want. I understood you want to align using a reference transcriptome and obtain a bam mapping, though it is not clear if a reference transcriptome built from your own reads, or one derived from the standard reference genome and annotation. If you do not want to align to a transcriptome and instead want something else, you will have to spell out clearly what you want.
Do you want to align to a reference transcriptome, and obtain bam files? Salmon can do that, as BWA or Bowtie.
Do you want to assemble a reference transcriptome (with Trinity / Velvet+Oases / etc) from your reads, align the reads to it and obtain a bam file? Again, Salmon, BWA or Bowtie can do that.
With STAR, you can align to a reference genome and output the mapping to the transcriptome.