We have two samples are PacBio Iso-seq libraries so they are long read transcriptomes. The two samples are from the same cell line with the only difference being the parental line (WT) and knock down of a particular gene (KD). The question is: Does the knock down cause transcriptome-wide differences in isoform usage?
We have the SQANTI3 output from the facility. Can anyone please give me some suggestions how to answer the question? Thanks.