Hi,
I have a problem trying to focus on a specific gene to study for circRNA.
In my work, I have both control and diseased condition. I generated circRNA from circular RNA identifier (CIRI2) as well as "quantified" it with sailfish-cir for each condition. From my understanding, CIRI2 presents results based on gene level (Ensembl gene ID), and feature them in terms of coordinates. Sailfish-cir presents results based on transcript level. So their IDs are Ensembl transcript's. But a gene ID can have multiple transcript ID. So how does one consider which transcript to focus on? Rather, how does one make the comparison, or focus on which genes?
Another question is how does one interpret the TPM value presented in sailfish-cir? Does it mean a proportion of both circRNA and linear fragments per million transcripts? So if the disease has like a value of 5 for TPM and the control has 2, what does it really mean? How does one say it in layman terms?
Thank you.
