Hi Everyone, I am new to circRNA analysis, and I could use some help with clarification.

In summary, I have have paired end mouse samples that I have aligned using STAR. I have followed instructions on CIRCexploler2 tutorial and I have successfully parsed and annotated my STAR aligned samples. In my annotation folder, I have circularRNA_known.txt files output for every sample. I am now interested in getting count matrix to use for downstream analysis like DEG. I could really use some help figure how to get the counts from here. Thank you.