I'm a beginner in RNAseq analysis. I have been trying to find a particular isoform of a gene. I used STAR and cufflinks for mapping and assembly.
The blue ones in the picture are the isoforms present in the reference genome (hg_38) but the gray one is the isoform that I'm interested to analyze and it's not present in the reference genome. How do I detect this new isoform?
Hope I could get some help from the experts. Thank you!