Question: How does CIRCexplorer2 work with paired-end data?
gravatar for IP
3.6 years ago by
Denmark/University of Copenagen
IP690 wrote:

Hi everyone!

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,

rna-seq circrna tophat • 1.6k views
ADD COMMENTlink modified 3.5 years ago by kepbod90 • written 3.6 years ago by IP690
gravatar for kepbod
3.5 years ago by
kepbod90 wrote:

The latest version of CIRCexplorer2 has supported paired end datasets. See for details.

ADD COMMENTlink written 3.5 years ago by kepbod90

Yeah, I know (I have use it and I got very interesting results). My question is how does it work theoretically with paired-end data. Does it aim to identify only backspliced junction reads? Or does it take another kind of information into account? like in this case:

The right part of the read will map in the genome before the left part

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by IP690
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1544 users visited in the last hour