I am working on transcript level expression from RNAseq using cufflinks after STAR alignment. I am primarily interested in a gene which has a wild type transcript and a novel transcript.The wild type transcript has the coordinateds and is known so it is present in the gencode annotation file,so I have been able to calculate its expression value.
But , I also want to calculate expression of novel transcript for which I have only fasta sequence.How can I accomplish this? And also I know which exons its made up of compared to the wild type.
For e.g. if wild type has 6 exons,the novel transcript has 3 exons.