FAQ

Q: Which aligners does CIRCexplorer support now?

A: The latest CIRCexplorer supports TopHat/TopHat-Fusion and STAR.

Q: The famous circular RNA CDR1as is not in my results even though I have the CDR1 annotation in the ref.txt. Why?

A: Firstly, CDR1as is cell-specific expressed and it could not be detected in many cell lines. Secondly, the boundaries of CDR1as and CDR1 are not consistent, and CIRCexplorer will output all the circular RNAs with exactly same boundaries with gene annotations. If you want to get circular RNAs with inaccurate boundaries, you could add the --no-fix option, but please notice that the permitted bias is +/-10bp.

Q: Does CIRCexplorer support paired-end reads?

A: CIRCexplorer was originally developed to support single-end reads, and does not require extra information from paired-end reads. So you could simply merge paired-end reads as single-end reads to do the analysis.