I have been using CIRCexplorer2 in single-end RNA sequencing datasets for a while, however, I have never use it for paired end data. In the papers and suplementary methods of circexplorer and circexplorer2 it is clearly explained how does the program identify circRNA in single-end datasets. It aims to identify the backspliced junction read of the circRNA, that's it, a read that maps in a non-colinear order to the genome.
However, for paired end datasets, using tophat-tophat-fusion, I think that there could be different aproaches to identify circRNA, as one could have, different indicators for circRNAs, for example:
- The left reads with the backsplicing read and the right read mapping to an exon.
- The right part of the read will map in the genome before the left part
Does anyone know how does CIRCexplorer2 adress this problems?
Thanks for reading,