Perform differential circular RNA expression

Question

[wangdp123]

Hi there,

I am using CIRCexplorer2 to annotate circRNAs from the paired-end RNA-Seq datasets and obtain a file named "circularRNA_known.txt" with the column of number of junction reads.

1) What is the cutoff to defined the expressed circRNAs according to the number of junction reads of each annotated circRNAs?

2) How to perform the differential analysis between two groups of samples based on the number of junction reads?

3) How to calculate the RPM (Reads Per Million mapped reads) based on the paired-end data as I have been aware that CIRCexplorer2 will convert paired-end reads into single reads before doing the analysis?

Many thanks,

Tom