My question is that can I use cufflinks to calculate cassette exon inclusion rate. Cufflinks output file transcripts.gtf provides isoform expression, is it reasonable to calculate cassette exon expression as the sum of FPKM of the isoforms containing the exon, and gene expression as the sum of FPKM of all the isoforms which belong to the gene, then take the ratio as cassette exon inclusion rate?
I wonder whether this method is accurate enough compared with using junction reads to calculate cassette exon inclusion rate directly.
I wonder whether this method is accurate enough compared with using junction reads to calculate cassette exon inclusion rate directly.
Comment