Hi all,
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.
Thanks, Ron
Hi Seidel,
Thanks for your response.I thought about creating a novel Transcript ID and use the necessary exons of interest.But I was not sure since this gene above has FPKM of 0.63 as well as all the exons. So if I just take a few of those exons for novel transcript ,wouldnt the expression be same again ? Since all these exons have same expression and hence resulting in the same mean expression of this gene.