my favorite transcript is supposed to consist of 12 exons (it was only described in germ cells, not in somatic tissues). Thus, I want to check what isoforms are actually expressed in my (somatic) tissue of interest.
I have paired-end RNA Seq data from a larger number of samples. I would like to use this dataset to shed light onto the isoform.
Thus far, I have aligned my reads using STAR, and counted exons using featureCounts. Seemingly, only a few exons are expressed, but quite consistent over all samples. There is no described isoform of the transcript that looks like what I have.
How would you suggest to go from here to obtain a consensus sequence? Do I need to assemble the whole transcriptome, or are there any shortcuts I can take, as I am only interested in a single transcript?