I am starting differential expression of circRNAs. I have used DCC and CIRI2 and have selected circRNAs detected by both methods.
Do I use read counts from DCC or CIRI2 for differential expression in DESeq2?
I don't think the average of read counts from DCC or CIRI2 is correct as they are different tools. The papers I have read are not that clear with what they do.