Hi,

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.

Haiyan

The purpose of the Bioconductor support site is to help with technical problems related to Bioconductor packages. Figuring out the biology behind your experimental observations, especially with the given (=bascially no) details, is really not something strangers on the internet can help with.